Genetic characterization of lentil (Lens culinaris Medik.) cultivars is important for lentil breeding. Therefore, random amplified polymorphic DNA (RAPD) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis were carried out to evaluate genetic diversity in 13 Turkish lentil cultivars. A total of eight RAPD primers were used in this study; 61 bands were produced and 55 of them were polymorphic (89.78%). The RAPD primers OPA-10, OPB-11, and OPI-13 had the highest polymorphism ratio (100%). As a result of SDS-PAGE analysis, variations in the seed protein pattern were observed among the lentil cultivars being studied. The SDS-PAGE similarity matrices indicated higher genetic similarity estimates among the lentil cultivars than RAPD. In addition, principal components analysis (PCA) was performed for both SDS-PAGE and RAPD where the first three components accounted for 75.760% and 68.121% of the total variation for SDS-PAGE and RAPD analysis, respectively. It was noted that the lentil cultivars with factor loadings greater than 0.5 for each principal component (PC) were also grouped together in the SDS-PAGE and RAPD dendrogram. In addition to genetic diversity, cotyledon color (an important market criterion) values were measured for lightness (L*), redness (a*), and yellowness (b*). As for cotyledon color, values for brightness, redness, and yellowness varied significantly among lentil cultivars. Among the red lentil cultivars, ’Cagil’ and ’Yerli Kirmizi’ had the highest cotyledon L* values of 70.83 and 70.74, respectively. The results of both genetic diversity analyses and cotyledon color of lentil cultivars would help in planning future breeding programs to improve high yielding marketable lentil cultivars.