A strong xylophagous activity of termites depends on the symbiotic relationship between termites and microorganisms inhabiting their guts. Particularly, symbiotic protists in the gut of so-called (phylogenetically) lower termites play a major role for cellulose digestion. However, few studies have investigated the energy metabolism of termite-gut protists because they are very difficult to culture in laboratories. Our goal is the elucidation of energy metabolism of the symbiotic protists to understand the effective utilization of woody resources. We identified the genes encoding enzymes homologous to members of glycolysis and energy production by meta-EST analysis of the mixed population of symbiotic protists in the gut of the termite Coptotermes formosanus, which harbors only three species of protists in the phylum of Parabasalia that carry anaerobic energy-generating organelles, hydrogenosomes. One remarkable point was the process to produce malate. We identified only one clone of pyrophosphate dependent pyruvate dikinase that involves in the final step of glycolysis to produce pyruvate, whereas we found 25 clones of phosphoenolpyruvate carboxykinase (PCK) and 24 clones of malate dehydrogenase (MDH) from total 2,136 EST clones, suggesting that malate　was mainly produced in cytoplasm and transported to hydrogenosomes. The reducing equivalents produced during the degradation are efficiently transferred to hydrogenosomes by malate and eliminated there by hydrogenases. The PCK genes were phylogenetically divided into two distinct parabasalian groups, and each of the two groups was closely related to bacterial PCKs, suggesting multiple horizontal gene transfers from bacteria.