The genus Gouania is endemic to the Mediterranean Sea and is a representative of rare European vertebrate fauna which exclusively inhabits pebble beaches. Until 2019, this fish genus was considered monotypic, but recent phylogenetic and taxonomic research proved the existence of five species, two of which inhabit the infralittoral gravel of the northern Adriatic. Previous research has been related to the species Gouania willdenowi, but due to its redescription and description of the new species the need for new ecological research arose. Gouania pigra and Gouania adriatica are sympatric species which inhabit the interstitial space of pebble beaches of the northern Adriatic and the aim of this study was to investigate the differentiation of niches of their microhabitat. In this research, the beaches at Sveta Marina, Krnička Luka bay and in Pula, where the presence of both species was previously determined, were sampled. Gravel was sampled at random with a bucket and individuals of the genus Gouania were sought among the gravel. Identified individuals of the genus Gouania were determined and measured, and gravel was sifted through a series of sieves. Statistical processing and analysis of the data has determined the investigated differences in the microhabitat of these two species. An overlap in the niches of G. adriatica and G. pigra was found, but with an increase in body size, partitioning was established in the largest sediment fractions. Along with the body size, several granulometric parameters were found to influence the selection of the suitable microhabitat. Gouania pigra is endemic to the Adriatic and a better knowledge of its habitat, which is under extreme anthropogenic pressure, will help in its adequate protection.