Coicis oil is one of the main functional substances of coix seed， and fatty acid is an important component. The contents of stearic acid， oleic acid and linoleic acid in seed kernels of 190 coix germplasms from 9 provinces in China were detected. ClSAD and ClFAD2 sequences polymorphisms were analyzed and the haplotypes were identified. The haplotype association analysis of fatty acid content was carried out. The results showed that there were wide variations in the content of three fatty acids in the seeds of different coix germplasms， the coefficient of variation was 15.84 % - 23.05 %， and the genetic diversity index was 5.22 - 5.23， among which the content of oleic acid was the highest and the content of stearic acid was the lowest， and there was a very significant positive correlation between the fatty acid components. There were 14 SNPs and 3 SNPs in ClSAD and ClFAD2， respectively， and 5 haplotype have been identified. The ClSAD haplotype Hap3 and ClFAD2 haplotype Hap1 are consistent with the reference genome， respectively. Hap3 of ClSAD was significantly associated with stearic acid content and had a negative effect on the conversion of stearic acid to oleic acid. Hap1 of ClFAD2 was favorable for linoleic acid accumulation， while Hap2 was significantly associated with linoleic acid content and had negative effects on linoleic acid synthesis. One key SNP locus was identified in each of the two genes， which was the key locus to the difference of SAD and FAD2 enzyme activity. The results will provide a theoretical basis for the breeding of high oil coix varieties， as well as the development of molecular markers and the analysis of related molecular mechanisms.