The availability of information regarding breeding and molecular aspects of African marigold (Tagetes erecta L.) is rare, and a very few hybrids have been developed for this economically viable crop. A study was conducted using 13 parental genotypes (3 male sterile lines and 10 testers) of African marigold to develop 30 F1 hybrids, and the true hybrids we evaluated based on phenotypic and marker-based genotypic data. Analysis of variance revealed significant diversity among the parental lines for different growth and flower traits. Fourteen SSR markers were used to test the purity of selected F1s, out of which two markers (TE57, T93B) showed polymorphism in the parental lines and cross combinations, with 2–5 alleles. The markers, TE57 and T93B revealed polymorphism information content (PIC) of 0.345 and 0.543 (mean 0.444), respectively, and detected a heterozygosity mean value of 0.528 in all, indicating the efficacy of microsatellite markers in discriminating the hybrids. The phenotypic data revealed significant difference in means for both quantitative and qualitative traits between the parents and the hybrids, in support of the molecular outcomes pertaining that hybrids detected through microsatellite markers were pure F1s. The study identified a set of compatible cross combinations that can be used to develop highly heterotic hybrid combinations with different growth and flowering characteristics.