The fatty acids of anaerobic bacteria were detected by ion chromatography (IC). The results showed that 11 kinds of standard fatty acids could be analyzed within 15 min, and just needed 1 injection sample. The fatty acids patterns of 40 strains of anaerobic bacteria detected by IC were essentially the same as that by gas chromatography (GC) reported by VPI. In comparison with GC, IC has further advantages: pretreatment is simpler, both volatile and non-volatile fatty acids can be analyzed at the same time, and formic and lactic acid can be well analyzed.