The external morphology of native (Bulgarian) and non-native (Slovak) populations of Neogobius melanostomus was examined using standard distance-based measurements and, in addition, comparison of fin ray number between populations was made. Five of the 29 morphological characters measured differed between populations, both for males and females. The non-native population was characterised by a smaller mouth and eye, shorter pre-dorsal distance and greater inter-orbital distance. Three characters, post-orbital distance, head depth and minimal body depth, differed between populations only in females, though the overall trend was the same in both sexes. A lower head depth value, greater post-orbital distance and minimal body depth was recorded for females from the non-native population. The range in fin ray numbers was similar between native and non-native populations. Populations differed, however, in the frequency of pectoral fin rays. Individuals with 17 pectoral fin rays were more common in the non-native range, their proportion in the native range being low. In contrast, individuals with 19 pectoral fin rays occurred more commonly in the native range. This difference was consistent for both sexes. The differences between populations are discussed within the context of differing environments and the “ship transport” hypothesis.