Diptera - True Flies
Though many insects are called flies - such as dragonflies, butterflies and fireflies - only insects in the order Diptera ("two-wing") are considered true flies. This may seem confusing until you consider that you are already familiar with many common types of true flies: house flies, horse flies, blow flies, and mosquitoes (also flies). In fact, about one in ten species on Earth is a true fly (~150,000 described species)! Flies live in almost all habitats except the open ocean, even venturing into hot springs, tar pits and Antarctica. They do many things and eat many types of food, but most are harmless to humans and rarely come in contact with us. Some, however, are serious pests of crops and deadly parasites of animals (including humans).
Flies are considered to be the most ecologically diverse order of insects. They have an egg, larval, pupal and adult stage, just like other holometabolous insects , so the free-living stages (larvae and adults) often do different things.
Since the larvae are the ones doing the most growing, they are more important when it comes to diet. The majority of fly larvae feed on decaying matter, eating the microbes (such as bacteria and yeasts) found in composting materials; these can include rotting plants, fungi, animal carcasses and dung. Other larvae are more particular about what they eat and how they go about doing it. Some are predators, feeding on other insects and invertebrates (though some large horse fly larvae can feed on small frogs and toads!). While many hunt their prey, certain fly larvae capture prey in silk (like some predatory fungus gnats ), use pits dug in fine sand (flies called worm lions ), or use their antennae to grab prey (phantom midges )! Many fly larvae are parasites or parasitoids of other animals. Parasites (things that do not directly kill their host) include maggots that suck blood, and ones that live in animal flesh (including bot flies, Oestridae). Parasitoid species (things that parasitize a host, killing it in the process) infest many animals including other insects, worms, millipedes, and wood lice, to name a few. Some important parasitoids are useful for killing pests, such as tachinid flies (wide range of pests) and many families that attack scale insects and soft-bodied Hemiptera. Lastly, many fly larvae attack and eat healthy plants. They can feed on various parts of the plant and some actually cause the plant to produce strange growths, called galls . Plant-feeding flies can become destructive crop pests (as described below), but some are used to control weeds.
Adult flies are less diverse in their feeding habits. Most will take wet, sugary substances, like sap, nectar and honeydew (sweet liquid produced by other insects). Some are predators, capturing prey in flight or in short bursts on a substrate. They often they have piercing mouthparts which they use to impale the (usually) insect victim. Other flies are adapted to suck the blood of animals. Some fly in, land and take a meal of blood (e.g. horse flies or mosquitoes), while others live as external parasites in the fur or feathers of their host (e.g. louse flies). Blood-feeding is only done by females in the lower Diptera and lower Brachycera (below 2 on tree; below right), while blood feeding in higher flies occurs in males and females (e.g. Muscidae and Hippoboscidae).
True flies display many different biologies, feeding habits and lifestyles, too many to describe here. More information can be found in the family sections (links at bottom), and further information can be found through the references and links.
What do flies look like?
Flies come in many different forms, but are all characterized by having only two wings as adults (most insects have four), when their wings are present (see Hippoboscidae  or Braulidae for examples without wings). The hind wings of flies are reduced to knob-like appendages called halteres (hall-TEERS)  that are used to balance them while flying - this is the reason they are among the best-maneuvering insects in flight. Flies are also generally known for having softer mouthparts used for sponging or sucking, rather than biting/crushing mandibles. To further describe flies it is best to break them into their two main groups: lower Diptera and Brachycera (see tree at right). The lower Diptera (below 1 on tree) were historically called Nematocera ("thread horn") because of their usually long, many-segmented antennae. Flies in this group normally have thin legs and bodies, have wings with many wing veins, and are slow fliers. When you think of these flies imagine mosquitoes, crane flies, and midges. Flies in the group Brachycera ("short horn"; above 1 on tree) are generally heavy-bodied, with short antennae (many aristate ) and a reduced number of wing veins. These flies are more familiar, including horse flies, house flies, and fruit flies. While all fly larvae share the characteristic of lacking true, segmented legs on their thorax (most other insect larvae - such as caterpillars and beetle grubs - have true legs), the larvae of these two groups also differ. Larvae of lower Diptera usually have a well-developed head, and pupae that somewhat resemble the adults. In Brachycera, larvae have reduced heads, so much that in some cases (particularly Cyclorrhapha; above 2 on tree) only the retractable mandibles (called mouth hooks because of their appearance) and internal rods exist as their "head". Pupae of many Diptera (Cyclorrhapha) are formed inside the last larval skin, called a puparium.
Male and female flies also differ in appearance (called sexual dimorphism), and sometimes knowing the sex can be useful (for example, if you are using pheromone traps to attract one sex). Two of the most common differences occur on the head. The first is where males have large eyes that may take up most of the head and touch each other (described as holoptic ), while females have normal-sized eyes (described as dichoptic ). The other difference occurs mostly in lower Diptera, where male antennae are much more fuzzy or feathery (plumose), than females who have more normal antennae with short hairs (right). However, both of these rules are not universal throughout flies.
Flies go through the normal life cycle of other holometabolous insects: they have an egg, larva, pupa and adult. As mentioned above, lower Diptera generally have four larval instars and pupae that look somewhat like undeveloped adults; many lower Brachycera are similar. A large and successful group of Brachycera, called Cyclorrhapha, differs in that they have three larval instars and pupate in the last skin of the larva; their pupae often look like inflated larvae. These are general life histories, but there are many different ways of reproducing in flies. For example, certain flies give birth to young or fully-grown larvae (e.g. Hippoboscidae and Sarcophagidae), while some species (some members of Sciaridae and Cecidomyiidae) have larvae that are able to produce their own offspring!
How would you take a good diagnostic picture of a fly?
Since flies range in size from smaller than a freckle to over an inch or two, some are easier than others to capture in photos. Some larger, common flies can be identified from a photo of the whole insect. Others are best identified using a number of more-specific features. The pattern of wing veins (venation) is extremely important. Close-up photos of fly heads showing the antennae, eyes, mouthparts and bristles are equally as important. The thorax can be very useful for its bristle or scale (mosquitoes) arrangement. Some flies can only be determined to a certain species using the reproductive organs at/in the tip of the abdomen. For lower Diptera, external genitalia are somewhat easier to photograph with the right equipment. For other flies the genitalia must be dissected to see the internal parts. Larval lower Diptera and lower Brachycera can often be identified to at least family using a photo of the body. However, many maggots (Cyclorrhapha) are almost impossible to identify under a microscope, let alone a photo. For maggots, usually only closeups of the rear spiracles, internal head and mouthparts, and finger-like front spiracles can help identifications. Lastly, some flies, like leaf miners and gall makers, can be more easily identified using their feeding patterns and effects on the plant, so be sure to photograph or preserve evidence of damage to the commodity.
Even with the best photos flies are notoriously difficult to identify, so collecting them can be useful if you need a positive identification from an expert. However, despite their annoyances, flies are relatively fragile insects that are easily destroyed, making them harder to identify. Most flies cannot bite you in aggression (only some robber flies and some rarely encountered horse fly larvae) so don't be afraid to lightly collect them using a paper towel or tissue - this will keep them intact. To keep specimens, freeze them in a plastic zipper bag or kill/store them in rubbing alcohol.
How do flies cause damage?
Flies damage plants in many ways, mostly during the larval stage. Many feed directly on the plant, including the roots (e.g. Bibionidae and Anthomyiidae), stems, flowers or fruit (e.g. Tephritidae; left). Others mine the leaves, living and feeding in the tiny space between the upper and lower surfaces (e.g. Agromyzidae; right). Some lay eggs in plants and cause them to produce growths called galls - the larvae then live and feed inside these "tumors" (e.g. Cecidomyiidae). Sometimes, the act of oviposition by females causes cosmetic damage or secondary infections (e.g. Tephritidae), because the females often have sharp egg laying devices to pierce the skin of fruits and other plant parts.
Very specialized flies can infest bee hives, where they cling to workers and rob them of their gut contents by causing them to regurgitate (Braulidae). Other flies are also known to live in bee hives and some actually parasitize honey bees (though they are not common or generally important as pests).
Flies that attack humans, livestock and pets, usually take blood meals or infest the skin of their hosts. Flies that drink blood do so by either slicing the skin of the victim, and lapping up the blood (e.g. Tabanidae and Simuliidae), or by piercing the skin to suck the blood (e.g. Culicidae; left). While feeding, these insects sometimes transmit diseases to their host (other flies can transmit diseases by transferring bacteria or viruses in their saliva or on their legs). Some flies (e.g. Oestridae) infest the skin of animals as larvae (termed myiasis, my-eye-a-sis), feeding off of the blood, secretions and flesh in the host’s wound. Livestock that are attacked can become sick and stressed, producing less milk, body mass or usable resources. The scarring around these wounds (“warbles”) can also cause imperfections if the animal’s hide is needed for leather. In severe cases, usually involving screw worms (some Calliphoridae), larvae burrow and feed on healthy tissue causing damage and sometimes mortality.
How to identify immature flies:
Fly larvae are extremely variable so there is no simple way to identify all immatures. The only real rule is that fly larvae never have true, jointed, thoracic legs (right). In the rare cases that they do have legs, they are always simple and fleshy (called “prolegs”; for an example see ). However, most fly larvae you encounter will not have prolegs.
Larvae of lower Diptera often look like worms or legless caterpillars (right), or highly adapted to aquatic habitats (e.g. mosquito or black fly larvae). They usually have a dark, definable head. Gall midge larvae often have reduced heads and resemble small to tiny, ridged, orange or pale grains of rice.
Most fly larvae in Cyclorrhapha are referred to as maggots. They are usually legless, with a pointy end (head) and a blunt end (tip of the abdomen) (below). Maggots are often pale/white and lack true heads, having only internal, hook-like mouthparts (mandibles) and a reduced head skeleton.
Common Families of Human Importance
There are many families of flies that are common and affect our lives either positively (beneficials) or negatively (pests). Since this page is just an introduction, please follow these links for specific information about these families:
Lower Diptera (Nematocera): mosquitoes, crane flies, fungus gnats and relatives
Brachycera 1: horse flies, fruit flies, and relatives
Brachycera 2: house flies, blow flies, and relatives
References & Links
Manual of Nearctic Diptera, Vols. 1-3. Agriculture Canada 
Diptera on Bugguide.net 
Database/Catalog of World Fly Species at Diptera.org 
Diptera.info (European Fly Website with IDs)