Few investigators have examined simultaneous bacterial and fungal responses to leaf-litter chemistry in fresh water. We tested the hypothesis that bacteria would be more abundant on labile litter with lower concentrations of defensive compounds, whereas fungi would be more abundant on recalcitrant litter. We used quantitative-polymerase chain reaction (qPCR) to measure the abundance of bacterial 16S and fungal 18S ribosomal ribonucleic acid (rRNA) genes and found that these groups responded differently to leaf chemistry. Bacterial 16S rRNA genes were 4× more abundant on labile than on recalcitrant litter. In contrast, fungal 18S rRNA genes were 8× more abundant on recalcitrant than on labile litter. Peak bacterial gene abundances on day 6 were related to leaf-litter % bound condensed tannin (r²  =  0.38), and peak fungal gene abundances on day 14 were related to % soluble condensed tannin (r²  =  0.49), % bound condensed tannin (r²  =  0.34), and % lignin (r²  =  0.33). Leaf-litter C∶N ratios were not associated with microbial gene abundance. The ratio of fungal 18S:bacterial 16S genes also increased along the 1^st axis in a principal components analysis of phytochemical variables. The early peak in bacterial rRNA gene abundance may indicate the role of bacteria in the early decomposition of leaf litter. rRNA gene abundance patterns demonstrate that bacteria and fungi have different patterns of growth and productivity in response to leaf-litter chemistry.