Understanding shallot seed systems is crucial for managing crop biodiversity on-farm where it is of both private value to farmers and social significance for future crop improvement and the resilience of the farming system. Focus Group Discussion (FGD) was carried out in Cirebon-West Java, Brebes-Central Java, Bantul-Yogyakarta S.R and Nganjuk-East Java. In Java, FGDs estimate that the share of formal seed sector in the total shallot seed supply rarely exceeds 5%. Hence, the seed supply is heavily relied on the informal seed system in which farmers use their-own strategies, including farmer-saved seeds, farmer seed exchange, and farmer-managed seed production. In the meantime, FGDs indicate that both systems in general are still characterized by low quality seeds, limited clean/healthy seeds, lack of supporting qualified human resources, lack of supporting infra-structure, and low transfer of seed technology. Both systems actually have considerable strengths to be leveraged and weaknesses to be improved. Therefore, FGDs suggest that integrating and recognizing the coexistence of the formal and informal seed systems in the four shallot producing areas in Java should be embraced to optimize the mutual benefits between the two systems.