Synthetic pyrethroids (SPs) are widely used in both agricultural and urban regions for insect control. Unlike many other pesticides, SPs are chiral compounds consisting of stereoisomers. However, occurrence of isomer selectivity in environmental processes is poorly understood for SPs. We evaluated isomer selectivity in toxicity of cypermethrin (CP) to Ceriodaphnia dubia and in its biodegradation by microbial isolates and in sediment. Among the eight enantiomers, two enantiomers (1R-cis-alphaS and 1R-trans-alphaS) were found to be toxic to C. dubia. Bacteria strains isolated from sediment selectively degraded CP diastereomers and enantiomers. The trans diastereomers were preferentially degraded over the cis diastereomers. Of the two active enantiomers, 1R-cis-alphaS was degraded slower, whereas 1R-trans-alphaS was degraded faster than the other stereoisomers. Similar isomer selectivity was observed during CP degradation in whole sediment. Since ecotoxicity is likely caused only by the biologically active enantiomers, knowledge on isomer selectivity may improve our understanding of the ecological risks of CP and analogous SPs.