Ascochyta blight, a major lentil disease caused by Ascochyta lentis, inflicts ~16.2 million dollars of economic loss annually on the Australian lentil industry. The most effective, economic and environmentally sustainable strategy is achieved by using A. blight-resistant lentil cultivars. Broadening the current knowledge of the lentil molecular defence response mechanisms would assist in identifying and improving resistant germplasm. Changes in the gene expression patterns in response to inoculation with A. lentis were examined in a resistant (ILL7537) and susceptible (ILL6002) genotypes via ion torrent RNA sequencing (transcriptome profiling). Samples were collected and compared at 2, 6 and 24 hours post inoculation (hpi) with either a highly aggressive isolate (ALP2) or H2O treatment. The transcriptome was assembled and annotated to predict open reading frames, known genes, protein families and molecular functions. The differentially expressed (DE) genes were categorised based on their annotation into three main physiological classes: primary defence response, induced defence response and necrotic structural defence response. The highest number of DE genes was found between the resistant and susceptible genotypes, in particular at 24 hpi, which correlates with the differential physiological response to the pathogen. This study describes a comprehensive transcriptome analysis of lentil defence response to A. lentis. Major defence related genes, functions and pathways were identified and their specific expression in the resistant genotype was revealed.