: The classification and phylogenetic relationships of L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within L. : Seventy polymorphic SSR markers (out of 177 tested) were used to analyze 141 alleles and calculate genetic distances among accessions. Phylogenetic relationships were determined using MEGA software (version 11.0.13) and visualized in a phylogenetic tree. ANOVA in NCSS 12 was used for statistical analysis. Over 1000 inter-race crosses were conducted to assess boll-setting rates. : Distinct phylogenetic patterns were identified between subspecies and races, correlating with boll-setting rates. , , and showed no significant increase in boll-setting rates in reciprocal crosses. Cultivars Omad and Bakht, as paternal parents, yielded higher boll-setting rates. and displayed high boll- and seed-setting rates as maternal parents but low rates as paternal parents. Additionally, phylogenetic analysis revealed a close relationship between cultivars 'Omad' and 'Bakht' with race , indicating their close evolutionary relationship. : Reciprocal differentiation characteristics of subspecies and races, particularly and , should be considered during hybridization for genetic and breeding studies. Understanding the phylogenetic relationships among taxa is crucial for exploring the genetic diversity of this economically important species.