A seed sampling system is provided comprising an automated seed loading assembly operable to singulate seeds from a plurality of seeds or enable loading of individually stored seeds and an automated seed sampling assembly comprising at least one sampling module operable to remove tissue samples from one of the singulated seeds. The system also includes an automated seed transport assembly comprising at least one retention member operable to transfer the singulated seeds from at least one elevator unit of the seed loading assembly to the at least one sampling module of the seed sampling assembly. In connection therewith, the at least one sampling module includes multiple sampling locations, each associated with a sampler, where the at least one sampling module is operable to remove tissue samples from seeds at one of sampling locations while another one of the sampling locations is cleaned to remove residual seed tissue therefrom.