TMV (Tobacco mosaic virus) and TSWV (Tomato spotted wilt virus) are the most common virus diseases that causes loss of productivity in pepper cultivation. The most effective method in the fight against viral diseases is the use of resistant cultivars. This study was conducted to determine the similarities and differences of 120 Capia pepper lines in the S2 stage, consisted of local populations, standard and hybrid cultivars, in terms of morphological variation and to determine the resistance levels of the lines to TSWV and TMV. As a result of molecular analysis, genotypes 34, 35, 36, 46, 47, 48, 84, and 85 were found to be homozygous resistant to L4 allele and the Tsw gene. Cluster analysis and principal component analysis (PCA) were applied to determine the relationship between the lines determined as a result of single plant selection. A dendrogram was prepared to evaluate morphological similarity between the lines. In the cluster analysis, 10 groups were identified based on 25 variables. The PCA explained 69.9% of the total variation based on 10 PC axes. At the end of the study, morphological variability was found high among the pepper lines. This evaluation of plant trait variability can assist geneticists and breeders to identify populations with desirable characteristics for inclusion in pepper breeding programs. In addition, the levels of resistance to these two diseases are crucial for breeding programs aimed at developing cultivars resistant to diseases.