Nanoscale zerovalent iron (NZVI) can be used to dechlorinate trichloroethylene (TCE) in contaminated aquifers. Dehalococcoides spp. is the only microbial genus known to dechlorinate TCE to ethene as a respiratory process. However, little is known about how NZVI affects the expression of genes coding for reductive dechlorination. We examined a high-rate TCE-dechlorinating mixed culture which contains organisms similar to known Dehalococcoides to study the effects of NZVI on the expression of two model genes coding for reductive dehalogenases (tceA and vcrA). A novel pretreatment approach, relying on magnetic separation of NZVI prior to reverse transcription qPCR (to avoid RNA adsorption by NZVI), was developed and used with relative quantification (relative to 16S rRNA as endogenous housekeeping gene) to quantify reductive dehalogenase gene expression. Both tceA and vcrA were significantly down-regulated (97- and 137-fold, respectively) relative to baseline (time 0) conditions after 72-h exposure to chlorinated ethenes (0.12 ± 0.03 mg/L cis-DCE, 0.69 ± 0.11 mg/L t-DCE, and 0.54 ± 0.16 mg/L VC) and bare-NZVI (1 g-NZVI/L). However, coating NZVI with an olefin maleic acid copolymer (a common approach to enhance its mobility in aquifers) overcame this significant inhibitory effect, and both tceA and vcrA were up-regulated (3.0- and 3.5-fold, respectively) after 48-h exposure. Thus, NZVI coating might enhance the expression of dechlorinating genes and the concurrent or sequential participation of Dehalococcoides spp. in the remediation process.