In polygynous systems, such as that exhibited by reindeer Rangifer tarandus, mate choice can be difficult to disentangle from male intrasexual competition because male behavior may constrain female choice. Multiple mating may provide an avenue for female mate choice, though it is difficult to identify using behavioral estimators alone. Molecular techniques address this issue by affording ecologists an opportunity to reassess mating systems from a genetic perspective. We assessed the frequency and possible explanations for multiple mating in reindeer using a genetic approach to determine the success of observed copulations in a semi-domesticated herd in Kaamanen, Finland. Behavioral and genetic data were synthesized with population characteristics over a 7-year period to test the hypothesis that, if present, polyandry in reindeer is driven by sexual harassment from sub-dominant males. We observed multiple mating in 42% of females, with as many as 60% exhibiting multiple mating in certain years. We found no evidence that multiple mating resulted from sexual harassment by sub-dominant males, suggesting that it is likely a deliberate strategy among females. Conversion rate of copulations into paternities varied with male size, with smaller males more likely to experience mismatch than larger males. Female preference for larger males persisted despite the occurrence of multiple mating, possibly suggesting a mechanism for cryptic post-copulatory selection. We suggest further research to delineate the possible influence of cryptic post-copulatory selection and multiple mating to defend against infertility in exhausted males.