The fatty acid composition of the flesh of rainbow smelt (RS, Osmerus mordax) and ruffe (RF, Gymnocephalus cernuus), two small fish species inhabiting the Gyda River (Siberia, Russia), was assayed using a gas-liquid chromatographic method with an ionization detection system and high efficiency capillary columns. RS was found to be richer in the total fatty acid content than RF (21.5 vs. 7.07 mg g–1). The proportion of saturated fatty acids (SFA) was similar in the fish studied (29.2 % in RS and 29.6 % in RF) whereas the flesh of RS contained a higher proportion of monounsaturated fatty acids, MUFA (42.2 vs. 13.9 %), and a lower proportion of polyunsaturated fatty acids, PUFA (28.6 vs. 56.5 %) than RF. RS is rich in essential n-3 PUFAs (2610 and 2390 μg g–1 for docosahexaenoic and eicosapentaenoic acids, respectively). In RF, the atherogenic index (0.39) and thrombogenic (0.20) index were lower than in RS (0.59 and 0.27, respectively). The fatty acid profile of RS in the study area differed from that reported for the flesh of this species from a Canadian estuary probably due to substantial differences in the diet of RS in these habitats. A comparison among fish species from the Gyda River indicated that in terms of nutrition indices, RS has the highest similarity with the muksun Coregonus muksun while RF is closely related to the northern pike Esox lucius. Based on the results from this study, both RF and RS can be recommended for human consumption. In particular, RS may be used as a replacement for muksun, an overfished species, in the traditional diet of indigenous peoples in northwestern Siberia.