Sympatric populations are conspecific populations that co-exist spatially. They are of interest in evolutionary biology by representing the potential first steps of sympatric speciation and are important to identify and monitor in conservation management. Sympatric existence in freshwater habitats can be more easily defined than terrestrial ones, and a series of sympatric fish populations have been reported. Reviewing the literature pertaining to sympatric populations of salmonid fishes, we find that most cases of sympatry appear coupled to phenotypic divergence, implying ease of detection. In comparison, phenotypically cryptic, sympatric populations seem rarely documented. We explore the statistical power for detecting population mixtures from genetic marker data, using commonly applied tests for heterozygote deficiency (i.e., Wahlund effect) and the STRUCTURE software, through computer simulations. We find that both STRUCTURE and heterozygote deficiency tests are efficient at detecting population mixture only when genetic differentiation is high, sample size and number of genetic markers are reasonable, and the sympatric populations happen to occur in similar proportions in the sample. We present an approximate expression based on these experimental factors for the lower limit of FST, beyond which power for STRUCTURE collapses and only the heterozygote deficiency tests retain some, although low, power. The findings suggest that cases of cryptic sympatry may have passed unnoticed in population genetic screenings using number of loci typical of the pre-genomics era. Hence, cryptic sympatric populations may be more common than hitherto thought, and we urge more attention being diverted to their detection and characterization.