1. Dark diversity represents the set of species that can potentially inhabit a given area under particular ecological conditions, but are currently ‘missing’ from a site. This concept allows characterisation of the mechanisms determining why species are sometimes absent from an area that seems ecologically suitable for them.

2. The aim of this study was to determine the dark diversity of hoverflies in south‐eastern Europe and to discuss the role of different functional traits that might increase the likelihood of species contributing to dark diversity. Based on expert opinion, the Syrph the Net database and known occurrences of species, the study estimated species pools, and observed and dark diversities within each of 11 defined vegetation types for 564 hoverfly species registered in south‐eastern Europe. To detect the most important functional traits contributing to species being in dark diversity across different vegetation types, a random forest algorithm and respective statistics for variable importance were used.

3. The highest dark diversity was found for southwest Balkan sub‐Mediterranean mixed oak forest type, whereas the lowest was in Mediterranean mixed forest type. Three larval feeding modes (saproxylic, and phytophagous on bulbs or roots) were found to be most important for determining the probability of a species contributing to hoverfly dark diversity, based on univariate correlations and random forest analysis.

4. This study shows that studying dark diversity might provide important insights into what drives community assembly in south‐eastern European hoverflies, especially its missing components, and contributes to more precise conservation prioritisation of both hoverfly species and their habitats.