The projected increase in freeze-thaw frequency associated with warmer temperatures in the High Arctic could affect the dynamics of soil bacterial communities. We report here the effects of freeze-thaw (FT) cycles on High Arctic bacterial communities of soil samples collected from three sites with different depths of snow cover. Analysis of 16S rRNA gene amplicon sequences showed that bacterial diversity in soil sampled under high snow cover were significantly different from those under low snow cover and those with no snow cover, and showed little change in community diversity after nine consecutive FT cycles. Conversely, bacterial diversity in soil samples under low and with no snow cover decreased after the simulated FT cycles. It is therefore likely that reduced snow cover will influence soil bacterial community structure through an increased frequency of freeze-thaw cycling.