Changes in the intestinal flora and its metabolites have been associated with cardiovascular disease (CVD). Short-chain fatty acids, bile acids, and especially trimethylamine N-oxide (TMAO), an endothelial toxic factor produced by gut microbiota from phosphatidylcholine in meat, have been identified to be closely related to endothelial cell dysfunction as well as tightly affiliated with CVD, the two main types being coronary artery disease (CAD) and coronary microvascular disease (CMVD). We discuss how changes in the gut flora and the metabolite TMAO contribute to the development of CAD and CMVD. The above insight might serve as a stepping stone for novel CAD and CMVD diagnostics and therapies centered on microbiota.