Although polycrosses have been used to test the potential of cross-combination of a large number of sugarcane parents, the male parent of the half-sib progenies produced is unknown. The present study aimed to integrate the molecular marker technology to the sugarcane polycross approach by the application of microsatellite markers to identify the male parent of 41 elite clones derived from polycross families. Ten microsatellite [single sequence repeats (SSRs)] primer pairs were used to identify the most likely male parent considering markers present in the selected clone but absent in the female parent. The number of alleles generated by the 10 microsatellite primer pairs ranged from 102 (cross-pollination lantern 4) to 120 (cross-pollination lantern 2) with an average of 113.25 alleles per SSR. The average genetic similarity among the involved parents in the polycrosses was 45.9%. The results of the analysis of the SSR markers absent in the female parent and present only in the selected clone as well as the genetic similarity values allowed the identification of the most likely male parent in 73% of the total clones evaluated and also to detect probable contaminations. The obtained results highlight the importance of using molecular marker technology in the identification and confirmation of the male parent of high-performance clones derived from polycrosses in the sugarcane breeding programs.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)IAC (Instituto Agronomico de Campinas)Ctr Avancado Pesquisa Tecnol Agronegocio Cana IAC, Ribeirao Preto, SP, BrazilUniv Estadual Paulista, Fac Ciencias Agr Vet, Dept Ciencias Exatas, Jaboticabal, SP, BrazilPRDTA Ctr Sul APTA, Piracicaba, SP, BrazilUniv Estadual Paulista, Fac Ciencias Agr Vet, Dept Ciencias Exatas, Jaboticabal, SP, BrazilFAPESP: 08/56146-5