As locus-specific co-dominant PCR-based markers that allow semi-automated, high-throughput investigation technologies, microsatellites are ideal tools for genotype identification. Eleven of a set of 114 microsatellite markers available at the Agricultural Biotechnology Center proved to be suitable to distinguish between the parents of at least one of nine sweet pepper hybrid combinations. Markers with the highest information capacity were found to be capable of distinguishing between the parents of four different hybrid combinations and exhibited up to four different alleles in 18 haplotypes.