Because of their small size, black coloration, and the paucity of external characters, pipunculids are difficult to identify. It is particularly important to have male and female specimens from the same sample in order to associate the sexes. For secure identification it is necessary to dissect the male terminalia. To accomplish this, remove the abdomen and heat in 85% lactic acid for roughly 30 minutes. Remove the macerated abdomen and place it directly into clean glycerin. Dissection involves separating syntergosternite 8 from the remainder of the abdomen. Store the abdomen and dissected terminalia in glycerin in plastic microvials on the same pin as the source specimen. Surstyli shape, presence or absence of a membranous area on syntergosternite 8, phallic guide shape, phallus shape and ramification, sperm pump shape and sclerotization, ejaculatory apodeme shape, hypandrium shape and modifications of the sternites are often informative. In female specimens the ovipositor shape is often useful but few other diagnostic characters are available. Description of new species on the basis of females often complicates the taxonomy of the family and should be avoided unless new character systems are discovered for females.

In order to secure the ground color and pruinescence of pipunculids, specimens should ultimately be dried and pinned. Pinning fresh material killed with cyanide or ethyl acetate is the easiest and a number of techniques can be used. The best method for obtaining views of the insect's genitalia involves double mounting. Pinning through the right mesopleuron with a minuten, then pinning to pith is more expensive and time consuming than pointing, but produces excellent specimens that are less likely to require dissection than other pinning techniques. Note that the heads of pipunculids fall off very easily. Some collectors remove the head and pin it separately on the tip of the minuten. Material collected into alcohol is preferably dried with a critical point drier and then pointed or glued directly to the side of a pin. Chemical drying using HMDS (hexamethyldisilazane) or ethyl acetate is also acceptable. Although some researchers prefer to study pipunculids preserved in 70% alcohol, specimens preserved in this way discolor over time and become brittle and difficult to dissect.

A key to the genera of Pipunculidae is available in Skevington and Yeates (2001).