The enhancement in cayenne pepper (Capsicum frutescens L.) productivity is intently needed due to the ever-increasing demand, considered a vital vegetable commodity with complete nutrition and high economic value in Indonesia. Conventional plant breeding is one of the strategies to produce superior cultivars with increased yield. Thus, the latest research aimed to identify genetic diversity and gene inheritance patterns for selecting high-yielding F2 populations of cayenne pepper made through double and three-way crosses. The said research employed an augmented design combined with a randomized complete block design as an environmental design. The research factors consisted of non-repeating cayenne pepper (Capsicum frutescens L.) lines with a limited number of seeds originating from 10 parental populations. The resulting 100 and 52 F22 individual populations, obtained from double and three-way crosses, respectively, were evaluated in comparison with four control cultivars, i.e., Bara, Dewata, Ungara, and Katokkon. The non-repeated rows, divided into five blocks, included the control cultivars planted repeatedly in each block. The results indicated that almost all traits have high genetic diversity and heritability and have potential use as selection criteria. The traits plant habitus (0.135), stem diameter (0.202), number of productive branches (0.359), and fruit weight (0.171) have a direct utmost influence on yield compared with other traits; thus, these promising traits can serve as selection criteria along with yield.