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The evaluation of various desirable traits in eggplant genotypes has facilitated the efficient process of selecting and improving them. Morphological parameters have proven to be valuable in assessing the similarities or differences among different accessions, while molecular data have been used to support the conclusions drawn from the morphological analysis. This study was conducted to evaluate the performance of 42 eggplant genotypes collected from Malaysia, China, and Thailand. The characteristics under investigation were shown to be highly significant (p < 0.01) by analysis of variance (ANOVA). It was noted that the plants TV17 (5.59 kg) and MV18 (5.97 kg) produced large yields per plant. The SSR markers used exhibited moderate average values for the number of alleles (2.53). The major allele frequency displayed a high average value (0.53) and a moderate average number of effective alleles (2.31). Additionally, the observed Shannon’s information index, expected heterozygosity, and PIC were high (0.84, 0.54, and 0.45, respectively). Using the unweighted pair-group approach with arithmetic averages based on similarity matrices (UPGMA) Dendrogram, 42 accessions were sorted into five primary groups based on similarities. The findings of this study indicate that the use of simple sequence repeat (SSR) markers can effectively estimate genetic diversity and analyze phylogenetic relationships. Moreover, these markers can assist eggplant breeders in selecting desirable quantitative traits within their breeding program.