Related species often choose slightly different habitats to avoid competition. Three small, congeneric, diadromous, migratory gobioid fish (Genus Gymnogobius) from Eastern Asia, use different habitats from lower to middle reaches of relatively large rivers in mainland Japan. Though Gymnogobius also inhabits small islands with small streams, there is not enough space for them to segregate their preferred habitats. Therefore, it seemed likely that they adopt different habitat utilisation strategies. To explore this possibility, microhabitat and food habits of 3 Gymnogobius (G. urotaenia, G. opperiens, and G. petschiliensis) were surveyed in 31 streams on Sado Island, northern Japan from 2018 to 2022. To explore possible food resources, benthic communities were also surveyed. Microhabitat (flow velocity, water depth, stream width, substrate size and riparian vegetation) at each capture locality (n>900) were measured and compared using principal component analysis (PCA). Reproductive seasons of these gobies were estimated by collecting egg clutches in streams and by examining gonads. On Sado Island, all 3 goby species inhabited lower reaches of streams, but their microhabitats differed slightly in flow rate and water depth, especially during their reproductive seasons. Stomach contents of more than 500 individuals were examined and identified to the family level. Benthic organisms were collected quantitatively from the same streams and also identified to the family level. All three goby species were generalists, but specialized on prey taxa, such as chironomids, ephemeropterans and gammarids. Sampling points of their preferred benthos and microhabitats revealed similar stream environments. Notably, some terrestrial insects were also observed among their stomach contents, however. In conclusion, the three goby species used slightly different microhabitats in the same reaches of streams, associated with specific food resources. These characteristics represent different utilisation of the same habitat in small island streams.