Challenges in the emasculation of female parent panicles and limited morphological variation among canary seed (Phalaris canariensis L.) genotypes has resulted in a need for molecular markers to assess hybridity and seed purity. Codominant simple sequence repeat (SSR) markers can be used to assess hybridity and purity instead of a grow-out test. A set of 15 SSR markers was used to assess hybridity of 10 F₁-derived F₂ families developed from a cross between two glabrous lines: a yellow-seeded C05091 (female parent) and a brown-seeded C00038 (male parent). The two most informative SSR markers, CSM8 and CSM39, could confirm that 9 of 10 families were hybrids due to the presence of a marker allele from the male parent. Three SSR markers, CSM58, CSM85, and CSM102, allowed us to assess the genetic identity of four experimental canary seed lines: C08019, C08046, C09052, and C10022. The three markers also identified the physical admixture in 1 of 16 batches of seeds.