Ecological and life history characteristics such as population size, dispersal pattern, and mating system mediate the influence of genetic drift and gene flow on population subdivision. Bull trout (Salvelinus confluentus) and mountain whitefish (Prosopium williamsoni) differ markedly in spawning location, population size and mating system. Based on these differences, we predicted that bull trout would have reduced genetic variation within and greater differentiation among populations compared with mountain whitefish. To test this hypothesis, we used microsatellite markers to determine patterns of genetic divergence for each species in the Clark Fork River, Montana, USA. As predicted, bull trout had a much greater proportion of genetic variation partitioned among populations than mountain whitefish. Among all sites, FST was seven times greater for bull trout (FST = 0.304 for bull trout, 0.042 for mountain whitefish. After removing genetically differentiated high mountain lake sites for each species FST, was 10 times greater for bull trout (FST = 0.176 for bull trout; FST = 0.018 for mountain whitefish). The same characteristics that affect dispersal patterns in these species also lead to predictions about the amount and scale of adaptive divergence among populations. We provide a theoretical framework that incorporates variation in ecological and life history factors, neutral divergence, and adaptive divergence to interpret how neutral and adaptive divergence might be correlates of ecological and life history factors.