A set of 250 distinct, stable, and uniform backcross-derived inbred lines were developed in sunflower through 5 interspecific cross combinations involving 4 wild diploid annual species (Helianthus argophyllus, H. petiolaris, H. annuus, and H. debilis). The presence of the wild-species genome in these inbred lines was confirmed through higher chromosome associations (tri- and quadrivalents) at diakinesis. Maximum structural rearrangements of chromosomes were observed in lines derived from H. petiolaris. Forty morphologically diverse inbred lines along with 2 controls were subjected to measurements of phenotypic and genetic distance using 118 simple sequence repeat (SSR) markers of known map location. A total of 204 alleles were identified and the number of alleles per locus varied between 2 and 5. There were 46 unique alleles and the number of unique alleles was highest in the lines derived from the cross involving H. petiolaris. The polymorphism information content (PIC) values ranged from 0.05 to 0.575. The pair-wise comparison values based on genetic dissimilarity estimates computed using molecular marker data varied between 0.143 and 0.486 among the 42 lines. The results indicate that the sunflower gene pool could benefit from introgression of novel alleles from the latent genetic diversity present in the wild species and particularly through exploitation of the diploid annual H. petiolaris.