Short chain fatty acids (SCFA), are a crucial form of nutrition for digestion and assimilation of grass for ruminants including the yaks. Gut microbiota degrades chyme, produces SCFA and influences its proportion. Here, we investigated the fecal microbiota and SCFA concentration in wild yak (Bos mutus) and domestic yak (Bos grunniens). We hypothesize that yaks’ gut microbiota influence concentration of SCFA and in that way increase the assimilation of nutrients from the grass. Microbes and SCFA concentration of yaks were processed and measured by 16S rDNA and Gas Chromatography-Mass Spectrometry respectively. The results show that the yak fecal microbes are mainly composed of Firmicutes(66.47%, 68.38%)(wild yak and domestic yak respectively, the same below), Bacteroidetes(26.00%, 26.16%) and Proteobacteria(3.48%, 1.52%) at the phylum level. Furthermore, Ruminococcaceae(55.18%, 58.48%), Bacteroidaceae(8.75%, 9.59%) and Lachnospiraceae(7.57%, 6.14%) at the family level; the domestic yak has the similar mainly composition with wild yak. SCFA concentration (including acetic acid, propionic acid, i-butyric acid, n-butyric acid and n-valeric acid) in wild yaks’ feces are significantly higher than in domestic yak (P<0.01). Spearman correlation relationship analysis shows that there is strong positive correlation between Porphyromonadaceae, Bacteroidaceae, Paraprevotellaceae, Rikenellaceae, Erysipelotrichaceae and SCFA concentration in wild yaks (r>0.4, P<0.05). However, there only has weak positive correlation in domestic yak’s microbes. Our result suggests that the digestion of grass in wild yaks is more efficient than in domestic yaks.