Narwhal and beluga whales are important species to Arctic ecosystems, including subsistence hunting by Inuit, and little is understood about their mating ecology. Reproductive tract metrics vary across species in relation to mating strategy, and have been used to infer mating ecology. Reproductive tracts from beluga and narwhal were collected between 1997 and 2008 from five beluga stocks and two narwhal stocks across the Canadian Arctic. Tract length for males and females, relative testes mass for males, and tusk length for male narwhal were measured. We assessed variation relative to species, body size, stock, maturity, and season. Significant variation was found in testes mass across month and stock for beluga, and no significant difference between stock or date of harvest for narwhal. Beluga had significantly larger testes relative to body size than narwhal, suggesting they were more promiscuous than narwhal. A significant relationship was found between narwhal tusk length and testes mass, indicating the tusk may be important in female mate choice. No significant differences were found between narwhal and beluga reproductive tract length for males or females. The mating systems suggested for narwhal and belugas by our results mean the two species may respond differently to climate change.