A new Melanotaeniid species is described from 28 specimens collected from the Johnstone River, north Queensland. Melanotaenia utcheensis sp. nov. was found in sites with moderate to high water flow over cobbles and boulders and all sites are in close proximity to major agricultural activity and have moderately to highly disturbed riparian vegetation. Melanotaenia utcheensis sp. nov. has a distinctive colour pattern with a blue-black mid-lateral band and orange margins on vertical scale rows. It is morphologically distinct from the broadly sympatric Melanotaenia eachamensis (Allen & Cross, 1982) and Melanotaenia splendida splendida (Peters, 1866), as well as from its sister species from southern Queensland/northern New South Wales, Melanotaenia duboulayi (Castelnau, 1878). In particular, M. utcheensis sp. nov. has more first dorsal spines and fewer vertical scale rows and anal rays than M. s. splendida, and fewer soft second dorsal rays and more pectoral rays than either M. eachamensis or M. duboulayi. The new species is also generally smaller than either M. s. splendida or M. eachamensis and intermediate between them in eye diameter, predorsal length, head depth and body depth.