The high diversity of chili pepper (Capsicum annuum L.) in Mexico offers an excellent alternative to search for wild and semi-domesticated genotypes as sources of resistance to the complex Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae)-Begomovirus, which has caused enormous losses in commercial production of various horticultural crops. The goal of the present work was to characterize ex situ 18 genotypes of C. annuum from southern Mexico through 47 morphological descriptors, and to evaluate its response to the B. tabaci-Begomovirus complex. Morphological characterization showed the variables calyx annular constriction (CAC), number of branch bifurcation (NBB), and calyx pigmentation (CP) had the highest variation. Principal components analysis (PCA) of 47 morphological characteristics showed that 12 components were selected as meaningful factors. These components explained 94% of the variation. Cluster analysis showed three major clusters and seven sub-clusters. On the other hand, evaluation of the response to B. tabaci-Begomovirus showed that the genotypes have differential susceptibility to this vector-pathogen complex. Genotypes ’Chawa’, ’Blanco’, ’Maax’ and ’X’catic’ were into the low susceptibility to B. tabaci and low severity of viral symptoms. Surprisingly, the genotype ’Simojovel’ showed high susceptibility to whitefly, but was grouped into genotypes with low symptom severity. This study shows the potential of native germplasm of pepper to explore sources of resistance to the B. tabaci-Begomovirus complex.