Integrative taxonomy is a multisource approach that takes advantage of complementarities among disciplines and tends to make progress in species delimitation and diagnosis of cryptic diversity. Single-method approaches in taxonomic and systematic studies have many limitations, especially for diagnosis of cryptic species that can be overlooked. Cryptic species are morphologically indistinguishable (or almost), so a combination of molecular, ecological and subtle morphological characters, as well as phylogeographic and population genetic analyses have been proposed as a framework to diagnose and distinguish cryptic species. Our overview had three objectives: (1) to present potential limitations of recently used concept of integrative taxonomy in genera Merodon and Cheilosia; (2) to discuss further methods which can be applied to clarify the species borders in these two genera, beside morphology, geometric morphometrics of wings and male surstylus shape, and molecular data; (3) to underline potential taxa where integration of all available data can help to discover cryptic diversity.