[Objective] To explore the effect of methanogens on the carbon metabolism of anaerobic fungi.[Methods] End-metabolites of different carbon sources by two anaerobic fungi (Orpinomyces sp. and Neocallimastix sp.) with or without co-culture methanogens (Methanobrevibacter sp.) were compared after 96 h in vitro anaerobic batch fermentation.[Results] Co-culture F1 (Orpinomyces sp. +Methanobrevibacter sp.) greatly enhanced the production of methane, acetate and lactate after corn core and cassava fermentation compared to pure fungal culture F1^* (Orpinomyces sp.). In particular, lactate production by F1 reached (26.44±0.22) mmol/L when fermenting on cassava, 14 times more than those produced by F1^*. On the contrast, co-culture N3 (Neocallimastix sp. + Methanobrevibacter sp.) showed lower level of lactate production after corn core and cassava fermentation compared to the pure fungal culture N3^* (Neocallimastix sp.). In addition, lactate production varied greatly depending on the substrate amount and types of carbon. Lactate production by F1 showed an overall positive correlation with the amount of cassava, peaked (56.29±2.04) mmol/L when cassava amount was 2.0%. Besides, end-metabolites of five starch-rich materials fermented by F1 varied. In particular, there was a highly positive correlation (R₂=0.9554) between lactate yields and the proportions of amylopectin of substrates. Further fermentation on pure sugars by F1 was performed. Polysaccharide (maltodextrin) produced substantially greater amount of lactate than monosaccharide (glucose) and disaccharide (maltose).[Conclusion] Co-culture of anaerobic fungi with methanogens shifted the fungal carbon metabolism during fermentation, which depended on the carbon sources and fungal species.