Two pairs primers were designed base on the known sequence for amplification of FGF5 gene in the Inner Mongolian cashmere goats herd. It was found that a restrict fragment length polymorphism within the exon 1 of FGF5 gene from the second pair of primers using PCR-SSCP and PCR-RFLP. PCR products after recovered and purified, were sequenced that randomly selected from different genotypes. It was revealed a synonymous single base mutation (C-->T) for the AB genotype. The allele A was found to be predominant in Inner Mongolian cashmere goats and the allele and genotype frequencies in our sample coincident with the Hardy-Weinberg equilibrium. When analyzed for the association with fibre traits, this FGF5 SNP was found to have significant effect on cashmere fibre stretched length (P<0.01) and cashmere rate(P<0.05), but have slightly effect on others fibre traits (P>0.05). Cashmere fibre stretched length (P<0.01) and cashmere rate (P<0.05) in individuals of genotype AB was significantly higher than that in individuals of genotype AA.
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