The objective of this study was to evaluate the genetic effects involved in post-harvest water loss of C. baccatum fruits and to correlate fruit morphological characteristics. Fruits of eight landraces of C. baccatum and their twenty-eight hybrids were evaluated in a randomized, complete block design. Analysis of variance, diallel analysis, phenotypic and genotypic correlation, and path analysis for eight fruit traits were performed. Fruit width, fruit length, dry matter content, and fruit wall thickness were determined by additive gene effects. On the other hand, the non-additive effects played more important role than additive ones, including water loss, cuticle thickness, exocarp thickness, and total soluble solids. The relationship of fruit traits suggested that indirect selection can be carried out from field experiments under different environmental conditions. Overall, genitors 4, 24, 50, and 56 should be selected to form new populations to improve these traits. The Brazilian pepper landraces of C. baccatum species are a source of genetic variability for plant breeders, and the new segregating populations emerging through the crossing of pepper lines with reduced water loss should be developed, opening new ways for conventional breeding.