Bering Cisco Coregonus laurettae is an anadromous coregonine species known almost exclusively from northwestern North America and with only three documented spawning populations, all in Alaska. Previous studies of Bering Cisco phenotypic variation examined individuals collected primarily in coastal rearing habitats where population affiliation was not known. Here we compare meristic counts and morphometric ratios of pre-spawning adults among the three known populations: one each in the Yukon, Kuskokwim, and Susitna rivers in Alaska. We also compare meristic data with those previously reported for this species. Populations in the Yukon and Kuskokwim rivers were very similar, while the population in the Susitna River was significantly divergent for certain meristic counts and morphometric ratios. Our findings are consistent with recent genetic analyses that found the Susitna River population to be the most divergent of the three populations. While the Yukon and Kuskokwim river populations survived the Wisconsinan Ice Age in the Beringian Refugium, the Susitna River population colonized the drainage following ice retreat sometime in the last few thousand years. The population's divergence from the source population in the Yukon or Kuskokwim river could be due to a founder effect or adaptation to different environmental conditions.