The possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2 interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in co-cultures in which Geobacter sulfurreducens was the electron-accepting partner for either Geobacter metallireducens, which performs DIET, or Pelobacter carbinolicus, which relies on HIT. Transcript abundance for G. sulfurreducens uptake hydrogenase genes were 7-fold lower in co-cultures with G. metallireducens than with P. carbinolicus, consistent with DIET and HIT, respectively, in the two co-cultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET, but not HIT, was 240-fold higher in the co-cultures with G. metallireducens than with P. carbinolicus. The pilin gene pilA was moderately expressed despite a mutation that might be expected to repress pilA expression. Lower transcript abundance for G. sulfurreducens genes associated with acetate metabolism in the co-cultures with P. carbinolicus was consistent with repression of these genes by the H2 during HIT. Genes for biogenesis of pili and flagella and several c-type cytochrome genes were among the most highly expressed in G. metallireducens. Mutant strains that lacked the ability to produce pili or flagella or outer-surface c-type cytochrome Gmet_2896 were not able to form co-cultures with G. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more complex environments.