Perilla frutescens is a traditionally cultivated crop in East Asia that exhibits significant morphological variation between its two main variants: var. frutescens and var. crispa. To investigate the genetic basis of trait variation and segregation, we developed an F₂ population from a cross between weedy accessions of the two variants of Perilla and analyzed 107 individuals. Four qualitative and nine quantitative traits were evaluated, including leaf color, stem color, flower color, days to flowering, plant height, and leaf area. The F₂ population showed wide phenotypic variation. In the chi-square test for four qualitative traits, two traits (color of leaf reverse side, color of flower) followed a Mendelian segregation ratio of 1:2:1. Heritability analysis revealed high values for days to flowering and leaf width. In contrast, traits such as number of florets and leaf length exhibited lower heritability, indicating a more substantial influence of environmental factors. Hierarchical clustering analysis grouped the parental lines into distinct clusters, revealing a diverse distribution of F₂ individuals across multiple groups. Some individuals closely resembled one of the parents, while others formed novel clusters, reflecting recombination and the emergence of new trait combinations. These findings underscore the genetic complexity underlying morphological traits in Perilla and highlight the potential of weedy accessions as valuable resources for breeding. The foundation established by this study will aid in developing new cultivars with desirable traits.