In contrast with the past situation, the water buffalo currently is not only a draft animal, but also an important food source of milk and meat.As a meat source, it is increasingly apparent that water buffalo have huge potential for meat production, but studies on breeding need to be performed.To investigate the molecular mechanisms involved in the meat quality difference between the buffalo (Bubalus bulabis) and yellow cattle(Bos taurus), 12 chemical-physical characteristics of longissimus thoracis muscles (LTM) related to meat quality were compared at the age of 36 months; intramuscular lipid and b* (yellowness) were greater in LTM of cattle than in buffalo LTM, whereas a* (redness) was greater in LTM of buffalo.Gene expression profiles were constructed by bovine genome array.A total of 8,884 and 10,960 probes were detected in buffalo and cattle,respectively.A total of 1,580 genes were differentially expressed; 413 probes were upregulated and 1,167 probes were downregulated LTM of buffalo, which are mainly involved in ribosomal RNA (rRNA) processing,cholesterol homeostasis, regulation of transcription, response to hypoxia, and glycolysis.Quantitative real-time PCR was used to validate the microarray data.The enriched GO analyses of highly expressed genes in LTM showed that protein biosynthesis, striated muscle contraction, iron homeostasis, iron transport, glycolysis and glucose metabolism were shared between buffalo and cattle.High protein content, low fat content and deep meat color of buffalo LTM may closely associated with increasing expression of genes involved in cholesterol homeostasis and iron ion homeostasis, as well as reducing expression of genes involved in ubiquitin mediated proteolysisin and protein oxidative phosphorylation.These results establish the groundwork for further studies on buffalo meat quality and will be beneficial in improving water buffalo breeding by molecular biotechnology.