Use of a new class of molecular marker for evolutionary or conservation studies may promise improved information, but it may also call for reassessment of analytical methods and empirical limitations. We used DNA microsatellites to study population structure in Rocky Mountain bighorn sheep (Ovis canadensis canadensis) and to test the ability of microsatellites to distinguish bighorn subspecies. Genetic differentiation between bighorn populations was dramatically greater than in comparable studies of brown bears and grey wolves, and these species differences are consistent with known differences in habitat use and dispersal. In bighorn, however, statistical limitations make it difficult to distinguish between moderately and highly divergent populations. As a result, only gene flow estimates greater than about one migrant per generation (OMPG) are informative about true population relatedness. In bears and wolves, apparent differentiation is so low that migration estimates are greater than OMPG continent-wide, but factors other than high gene flow may contribute to these patterns. Despite analytical difficulties at large geographical scales and large genetic divergences, microsatellite data assist management by characterizing historical rates and patterns of dispersal on smaller scales, and by detecting population bottlenecks and regions of particularly high or low historical gene flow.