Herbicides are the most effective way to control weeds. Yet, the evolution of resistance in many weed species is a considerable threat to herbicide efficacy. Non-target-site-based resistance (NTSR) is the most threatening facet of herbicide resistance. NTSR is widespread, involves a variety of mechanisms, and can confer unpredictable resistance to herbicides, regardless of the herbicide mode of action. Because NTSR is endowed by differences in the expression of a number of genes in resistant and sensitive weed plants, few genes governing NTSR are currently known. This renders NTSR diagnosis and management tricky. The rise of next-generation sequencing technologies now enables extensive transcriptome comparisons between contrasting phenotypes of non-model plants such as weeds, which should allow the unravelling of the genetic mechanisms of NTSR. We implemented a transcriptomics-based approach to unravel the genes governing the NTSR of black-grass (Alopecurus myosuroides), a major weed in winter crops in Western Europe, to herbicides inhibiting acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase). The full transcriptome of herbicide-resistant and herbicide-sensitive plants was sequenced before, and at several durations after, herbicide application using the Illumina technology in a RNA-Seq approach. The sequence reads were assembled to generate a transcriptomics database for A. myosuroides. Sequence read mapping on the transcripts reconstructed in the database enabled us to identify genes for which expression was different in resistant plants compared to sensitive plants, or for which expression was differentially affected by herbicide application in resistant plants compared to sensitive plants. The expression patterns of the ca 40 most interesting candidate genes were checked by reverse-transcription followed by quantitative real-time PCR. This enabled us to identify the first set of candidate NTSR genes in a grass weed. This is a major step towards understanding the mechanisms underlying NTSR in A. myosuroides.