The present disclosure provides systems and methods for sorting seeds based on identified phenotypes of the seeds. In various embodiments, the system includes an optics and controller station structured and operable to collect image data of a top portion, a bottom portion and a plurality of side portions of each respective seed in a set of seeds, and to analyze the collected image data to determine whether each seed exhibits a desired phenotype. The system further includes a seed loading, transporting and sorting station structured and operable to singulate each seed of the set of seeds from a plurality of seeds in a bulk seed hopper, transport the set of seeds to the optics and controller station, and selectively sort each seed to a respective one of a plurality of seed repositories based on whether each respective seed exhibits the desired phenotype.