The faunistic analysis of soft bottom benthic materials collected from the Aegean and Levantine coasts of Turkey in August 2016 and 2017 revealed a total of 7 sipuncula species and 975 individuals belonging to 6 genera. The maximum population density of sipunculans was found to be 1790 ind.m−2 in the Aegean Sea and 730 ind.m−2 in the Levantine Sea. Onchnesoma steenstrupii steenstrupii was the most dominant species, comprising 83.1–92.8% of the total number of specimens in the Aegean Sea and 87.2–96.2% of the total number of specimens in the Levantine Sea. Four major sipunculan assemblages were found in the regions, and the main environmental factors controlling these assemblages were depth, temperature, salinity, the sediment grain size, nutrients and total organic carbon. Different abiotic factors affected the distribution of different sipunculan species in the regions. The present study included two cryptogenic sipunculan species; Apionsoma (Apionsoma) misakianum and Aspidosiphon (Aspidosiphon) mexicanus. •Relation between sipunculan species and environmental variables was investigated.•Depth, temperature, salinity, the sediment grain size, nutrients and total organic carbon affected the distribution of the sipunculan species.•Different abiotic factors affected the distribution of different sipunculan species in the regions.