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Angora and Cashmere goats are two breeds selected for fiber production, differing in hair follicle biology and fiber characteristics due to divergent selection. To explore the genetic basis of these differences, we used Whole Genome Sequencing (WGS) data from Cashmere, Angora, and non-fiber-producing goat populations. This enabled cross-population analyses to identify signatures of divergent selection between the three groups, as well as significant differences in allele frequencies.Cross-population analysis between Cashmere and non-fiber-producing goats identified 5,252 variants with divergent selection signals. Additionally, 2,414 variants were found between Angora and non-fiber-producing goats, and 326 between Cashmere and Angora. Three genes, <i>COL14A1</i>, <i>FGF5</i>, and <i>CUX1</i>, known for their roles in fiber biology, showed divergent selection across all three comparisons. Fisher’s exact test, applied to coding region variants with high or moderate predicted phenotypic impact, identified 735 variants with significantly different allele frequencies between Cashmere and non-fiber-producing goats, located in genes expressed in goat skin. In contrast, only 107 and 503 variants were found between Angora and non-fiber-producing goats, and between Cashmere and Angora goats, respectively, in genes also expressed in skin. These variants may contribute to phenotypic differences in fiber characteristics observed among the three populations.Although the effects of these variants remain unclear, our results represent an important step toward understanding the selection of fiber-producing goats.