This study aimed to trace the incorporation of 13C-labeled hydrophilic and hydrophobic compounds extracted from maize straw into bacterial and fungal phospholipid fatty acids (PLFAs) in upland and paddy soils. In both soils, the amounts of bacterial 13C-PLFAs recovered from hydrophilic C were 1.2–2.8 times higher than those from hydrophobic C. By contrast, the amounts of fungal 13C-PLFAs recovered from hydrophobic C were 3.8–12.8 times greater than those from hydrophilic C. These results indicate that bacteria have a preference for the uptake of hydrophilic compounds, whereas fungi prefer hydrophobic compounds in both soils. The fungal preference for hydrophobic compounds is stronger than bacterial preference for hydrophilic compounds. This is partly owing to the efficient incorporation of hydrophobic compounds into actinomycete PLFA of 10Me18:0 in upland soil and bacterial PLFA of 18:1ω7c in paddy soil. Consequently, the specific uptake of hydrophilic and hydrophobic compounds from plant residues by bacteria and fungi will lead to divergent C pathways in soil. © 2020 Elsevier Ltd