Abstract Toxic organotin compounds are widely present in the environment. Tributyltin chloride (TBT), an organotin, is degraded by a filamentous fungus Cunninghamella elegans. The major fatty acids of this fungus were: palmitate (16:0), stearate (18:0), oleate (18:1n9), linoleate (18:2n6) and γ-linolenate (18:3n6). We show that the fatty acid unsaturation index was decreased and the conversion of stearic acid (18:0) in oleic acid (18:1n9) was significantly inhibited in the presence of TBT. Changes in fatty acid compositions during TBT degradation at 10 mg l−1 in C. elegans revealed that the degree of saturation was correlated with biotransformation of the xenobiotic to less toxic compounds: dibutyltin and monobutyltin. Our results suggest that the high TBT resistance in C. elegans is associated with the modulation of the fatty acids composition and the biocide degradation.