Capillary electrophoresis-based genotyping platform and fluorescently-labeled primers were used to investigate the inheritance of six SMC336BS-primed SSR markers among 92 single pollen grains of variety L 99-233 and 165 zygotic progeny from the HoCP 00-950 x L 99-233 cross. Marker 6-154 was detected in one third of the pollens, while Markers 6-167, 6-169, 6-171, and 6-175 were amplified from half of the pollens showing an independent segregation pattern. Only 22 of the 32 expected pollen genotypes were observed at frequencies of 1.09% to 11.96%. On the other hand, all six SSR markers were detected among the zygotic progeny. Marker 6-166 was unique to the maternal parent HoCP 00-950, Markers 6-154, 6-167, 6-171, and 6-175 were unique to L 99-233, and Marker 6-169 was found in both parents. Markers 6-154, 6-166, 6-167, and 6-175 segregated at 1:1, Marker 6-171 segregated at 3:1, and Marker 6-169 segregated at 83:1. Although 64 genotypes were expected among zygotic progeny, only 36 were observed at frequencies from 0.61% to 8.48%. The data indicated that inheritance of SSR markers was complicated in sugarcane with the majority of SSR markers segregating in a 1:1 fashion. In addition, SSR markers of non-parental origin were never detected in both gametes and zygotic progeny. The discrepancies between expected and actual numbers of genotypes detected might be due either to the limited numbers of samples or to inability of all gametophytes transmitting into zygotic progeny.