Informal seed saving and farmer-to-farmer seed exchange are dictated by local rules and practices, which in turn can influence the distribution and management of crop biodiversity. Such systems are essential components of the livelihoods of small-holder farmers in Kenya and for in situ conservation of intraspecific and interspecific diversity. Using a mixed methods approach combining interviews, focus groups, and a household survey, we identify that the distribution of crop varieties in Tharaka, Kenya, has been shaped by both human migrations that have transported seeds and gender roles that have restricted travel and utilization of local indigenous varieties during early migrations. Our results suggest that the migrations of the first Tharaka people from Mbwa 300 years ago have influenced the concentration of local indigenous varieties in the areas of first settlement today. Subsequent smaller migrations dictated by men within Tharaka through the 1960s, particularly to the northern areas, originally limited the distribution of crops, such as pearl millet (Pennisetum glaucum), that are dependent on women for seed selection and processing. This study offers a specific case where the consideration of human migration and gender roles, currently and historically, have influenced the distribution of crop biodiversity, and thus farmer access, to specific types of varieties within a single region and ethnic group.