A comparative study was carried out in two different valleys of Ganga river system viz; Alaknanda and Bhagirathi. In both of valleys total 134 species with 118 genera and 56 families were recorded. Poaceae was the dominant family representing maximum (11) number of species followed by Asteraceae (10) Fabaceae (9) and Lamiaceae (9). In different vegetation strata a total of 39 species were encountered under tree layer, 36 species were under shrub layer and 59 species were under herb layer in both of the valleys. Out of them 31 tree species were recorded in Alaknanda valley and 27 were in Bhagirathi valley. In shrub layer 32 and 30 species were recorded in Alaknanda and Bhagirathi valley respectively. In the herb layer Bhagirathi valley showed highest (51) species richness in its influence zone and submergence zone (45). The proportion of family to species was recorded greater in both of valleys compare to the proportion of family to genus and genus to species.