Abstract Information on the distribution and vulnerability of invertebrates is often scarce and, as a consequence, this group of organisms is usually neglected in conservation studies. Yet it is possible to reasonably infer ranges and vulnerabilities of species and establish spatial conservation priorities, even with incomplete information. We investigated conservation priorities of hoverflies in Southeast Europe based on species distribution models (SDM) and vulnerability indices. Species distribution models were used to compensate for the lack of knowledge on species ranges. Measures related to geographical rarity, endemism and habitat specialisation were used to assess species vulnerability. Potential distribution and three alternative vulnerability indices were used to calculate two spatial conservation indices: potential Biodiversity Conservation Concern index (pBCC) and potential Biodiversity Conservation Weight (pBCW). pBCC highlighted areas with a large proportion of highly vulnerable species, even where species richness was low, such as the Danube delta and mid‐Aegean islands. It also identified potentially important areas yet‐to‐be surveyed (e.g. Carpathian mountains), which might deserve future conservation measures. pBCW emphasised areas hosting high richness of both vulnerable and resilient species, such as the eastern Aegean Islands and the eastern part of Crete. We demonstrate that: (i) it is possible to establish conservation priorities at large scales if SDM and simple vulnerability measures are combined; (ii) complementary approaches are necessary to emphasise the importance of areas with different characteristics; and (iii) several understudied areas should be targets of future sampling schemes to confirm their importance for the conservation of hoverfly diversity in Southeast Europe.