<p>Despite an increasing number of reports on rapid evolution driven by standing genetic variation (SGV) in natural settings, its prevalence in nature remains uncertain. <i>Telmatochromis temporalis</i> has independently developed a diminutive body size in two areas at the southern tip of Lake Tanganyika, forming a dwarf morph inhabiting shell beds. Assuming that this rapid parallel evolution is attributable to SGV, the dwarf allele of the responsible gene would be expected to persist at a low frequency in the ancestral normal morph, while increasing in frequency in the derived dwarf morph in these two areas. This study sought single-nucleotide polymorphisms (SNPs) consistent with this allelic pattern. Comparisons of genome-wide resequencing data from pooled samples between morphs and between areas identified 10 such SNPs, a number significantly greater than expected by chance, suggesting that these SNPs are subject to selection. Furthermore, three of these SNPs were correlated with variations in body size among genotypes of F₂ individuals derived from a normal F₀ male and a dwarf F₀ female. These three SNPs likely represent loci linked to the genes driving the parallel evolution of body size via SGV. This study presents a novel instance of evolutionary adaptation through SGV in natural environments.</p>