Recently, it has been recognized that methane oxidizing bacteria (MOB) provide food webs with carbon sources in boreal and temperate lakes. However, methanetrophic food webs is still largely unknown in tropical and sub-tropical lakes. In this study, we traced carbon sources for zooplankton in a sub-tropical Fei-Tsui reservoir, Taiwan in summer and winter, using fatty acid biomarkers, some of which are taxon-specific and assimilated into higher trophic animals with little or no modification. The fatty acids, 16:1n5, 16:1n8 and 18:1n8, have been widely used as the MOB-specific biomarkers in aquatic food web studies. We identified these three biomarkers for zooplankton, referring by fatty acid composition of cultured MOB (Methylocystis rosea, Methylobacter tundripaludum). For zooplankton, content of MOB-specific fatty acid biomarkers was 0.5 (mg/g dry mass) in summer, whereas it increased up to 3.6 (mg/g dry mass) in winter. Their content of algae-specific fatty acid biomarkers, in contrast, reduced from 14.9 (mg/g dry mass) in summer to 6.5 (mg/g dry mass) in winter. These results suggest that the MOBs serve as an important carbon source for the zooplankton in less productive winter.