A new species of Eleotris, a freshwater eleotrid, is described from streams of the Solomon Islands using both genetic analysis based on the mitochondrial COI gene and morpho-meristic study. The new species is separated from E. acanthopoma, E. melanosoma, and E. fusca with a mean pairwise divergence of 14%, 11%, and 9.9%, respectively. It shares with E. fusca, its sister species, the same combination of cephalic free neuromast patterns (i.e., second, fourth, and sixth suborbital free neuromast rows on cheek extending ventrally past horizontal row d (2.4.6 pattern) and row os connecting with row oi at ventroposterior margin of opercle, but it differs by a combination of characters including scales in lateral series 42–46 versus 53–67, transverse back series 11–13 versus 13–21, and zigzag series 9–11 versus 12–17.