Context. With growing World population, the demand for higher-yield crops becomes more evident. The genetic diversity, which is crucial for breeding superior cultivars, can be shown by using molecular techniques such as start codon targeted (SCoT) markers.

Aims. The motivation of this study was to unfold the genetic diversity of Turkish germplasm.

Methods. Ninety-four pea samples (90 landraces, 3 pea breeding materials, and 1 registered variety), were assessed for their diversity by using SCoT markers.

Key results. Eight SCoT markers produced a total of 84 scorable bands, of which 74 (88.1%) were polymorphic. There was an average of 9.25 polymorphic bands per primer. The range of diversity indices evaluated, such as polymorphism information content (0.13–0.38), effective numbers of alleles (1.22–1.69), Shannon’s diversity index (0.21–0.54), and gene diversity (0.13–0.38), showed great genetic variation in the germplasm under this study. STRUCTURE algorithm suggested the presence of two populations. Polymorphism percentage was 87% and 74%, whereas fixation index was 0.21 and 0.01 for population A and population B respectively. According to analysis of molecular variance, most of the difference was found to lie within population (99%) rather than between populations (1%). In contrast, principal coordinates analysis suggested separation into three populations.

Conclusions. The Nei’s genetic distance of 94 Turkish pea samples revealed that Antalya_2 and Canakkale_2 are genetically the most diverse and can be utilised as parental lines for breeding purposes.

Implications. The wide range of pea varieties found in the Turkish germplasm can serve as a valuable genetic resource for the overall pea breeding efforts.