Results/Conclusions Our recent diversity studies on flies (Diptera) of temperate forests have provided material of value for both ecological and taxonomic studies. Undescribed species have been dominant in some of these studies and are ecologically distinct from well-known, closely-related species. Quantitative analyses require standardized, replicated sampling whereas taxonomists often use directed collecting to target prime microhabitats. However, we have found that random sampling yields large numbers of taxonomically valuable specimens, especially in poorly-studied fly families such as Tipulidae and Mycetophilidae. Abundant species generally drive diversity patterns in assemblages; rare species are often omitted in diversity analyses, but these are the species that are of most interest to taxonomists. Undescribed species are not always rare. High ecological and trophic diversity in some families, such as Chloropidae and Phoridae, necessitates identification to species (or morphospecies in difficult groups), otherwise ecological patterns may be obscured. Species-level characters in many of these groups are cryptic and require taxonomic expertise. Deposition of voucher specimens is critical for subsequent verifiability of specimens, especially morphospecies. Vouchers are a potential future source of taxonomic data and voucher deposition should be promoted in ecological studies.