Five Chinese indigenous chicken breeds including BAI, LAN, XIS, YOU and TAI were treated as materials, then comparison of relative contents as well as factor analysis and clustering analysis of thirteen fatty acid index among the five chicken breeds were carried out. The results showed, TAI chicken breeds had the highest relative contents of Saturated Fatty Acids (44.96%), the following were LAN (43.26%),YOU (38.98%), XIS (38.56%), BAI (34.40%). There were significant difference (P﹤0.05) between relative contents of BAI and TAI, LAN. BAI chicken breeds had the highest relative contents of Unsaturated Fatty Acids (63.99%), the following were YOU (59.76%), XIS (59.45%), LAN (55.34%),TAI (54.43%). There were also significant differences (P﹤0.05) between relative contents of BAI and TAI, LAN. BAI chicken breeds had the highest relative contents of Essential Fatty Acids (6.76%),and it had significant difference（P﹤0.05）with relative contents of LAN (3.84%) and TAI (4.17%), but had no difference from that of XIS and YOU. The first three principal components obtained by factor analysis could account for 94.865% of all variations, and the percents were respectively 58.632%, 22.479% and 13.754%. The UPGMA dendrograms based on principal component values divided the five chicken breeds into three clusters, XIS, LAN and YOU were in one branch, BAI and TAI were in independent branches. The results of 3-D dendrograms were basically consistent with that of UPGMA dendrograms. These reflected the difference and advantage of muscle fatty acids property in five indigenous chicken breeds.