Freshwater populations of the Indo-pacific region are characterized by a large proportion of amphidromous species. In this paper, we analyse habitat selection by two amphidromous sympatric Gobiidae: Sicyopterus lagocephalus and Cotylopus acutipinnis in Reunion Island. A sampling method using Point Abundance Sampling (PAS) was conducted in 12 rivers. We used mixed logistic models in order to examine the presence probability of species according to location, downstream-upstream gradient, microhabitat variables (depth, velocity and predominant substrata) and presence of conspecifics and sympatric species. Presence probabilities varied between the sampled rivers. We observed a positive attraction between identical developmental stages of both species, which suggests that social interactions or similar preferences for environmental cues influenced their distribution. The presence probabilities of both species’ juveniles decreased from downstream to upstream. We showed that traditional microhabitat variables weakly explained the spatial distribution of both S. lagocephalus and C. acutipinnis, in Reunion Island. We suggest that weak habitat selection for these species is consistent with the amphidromous life style because of the unpredictability of juvenile settlement and the extreme hydrological variations in tropical rivers