Freshwater-fish populations of the Indo-pacific region are characterised by a large proportion of amphidromous species. We analysed the spawning-habitat selection of Sicyopterus lagocephalus (Gobiidae: Sicydiinae) within two rivers of the Reunion Island. Reproduction traces are rare events, so a presence-only sampling procedure was performed to collect egg clutches and a random description of available habitat was conducted to generate pseudo-absence data. Logistic models showed a strong selection for microhabitat variables and mesohabitat units. S. lagocephalus selected areas where availability of potential nests was high (small cobble to small boulder) and where interstitial substratum allowed intragravel flow. Our results suggest that the availability of favourable substratum may be a limiting factor, which could result in occupancy of suboptimal areas. Water depth and velocity had less of an effect on the selection of a spawning area. Higher selection for shallow (<60cm) and lotic (>30cms(-1)) geomorphic units, with an optimum for riffle and cascade, suggested that mesohabitat could be a satisfactory approach to quickly assess the availability of spawning areas within a watercourse for expertise studies.