This thesis examined historical and contemporary effects on genetic population structuring of prickly sculpin (Cottus asper) in British Columbia, Canada. A phylogeographic study was conducted, which disproved the traditional view that prickly sculpin survived the Last Glacial Maximum in only southern coastal and inland refugia, favoring allopatric divergence and giving rise to coastal and inland “prickling” phenotypes, which vary in the degree to which spine-like scales cover the body of the fish. Instead, analyses of mitochondrial DNA and microsatellite markers suggest parallel evolution of highly prickled inland populations, which presumably have evolved independently across three glacial lineages, originating from highly differentiated ancestral coastal populations. Postglacial colonization from coastal towards inland regions and associated founder effects resulted in decreased genetic diversities, which was also evident in a subsequent study on conservation genetics of a recently discovered peripheral population in the Peace River in Alberta. While no divergent “conservation designation unit” was detected in the Peace River, a for freshswater sculpins unusual high genetic connectivity over large geographic scales was found, which could reflect high dispersal capacities of an extended, planktonic larval stage that might have been at least partially retained from an amphidromous life cycle of the putative ancestral coastal populations. While such assumptions on life history characteristics of inland populations remain speculative, the divergence between coastal, amphidromous and inland, purely freshwater life cycles is young (< 14,000 years), and may be in an early, incomplete stage of a life history transition. To better understand life history transitions from amphidromous to freshwater life cycles in C. asper, a population genetics study was conducted in the Lower Fraser River system, which identified sympatric life history ecotypes represented by amphidromous sculpins in the river main channel, and genetically differentiated freshwater sculpins in the river tributaries. These results indicate that that isolation-by-environment to discrete freshwater habitats could play a role for the early stage of amphidromy-freshwater transitions, which may be further favored by the presence of large tributary streams and lakes allowing for large effective population sizes.