Computational analysis of the transcriptome data provided functional annotations to the gene models and gene families. We also identified gene loci harboring SSR and SNP sites and predicted their consequences on transcript structure, coding features and expression. To our knowledge, this study is the first to provide the relative expression of transcript isoforms in both etiolated seedlings and light-exposed green seedlings of cultivated spring accession DV92 and wild winter accession G3116 of T. monococcum. In order to preserve the granularity of the transcript isoform-based expression profile, we avoided projecting a weighted expression profile of the genes. This allowed us to identify a greater number of differentially expressed transcripts in G3116. However, for simplicity, the four-way Venn diagram was constructed to show comparison between the light up and down-regulated genes from the two accessions. Transcripts homologous to TaIAA1, an early auxin-response gene from wheat, were down-regulated by light in both DV92 and G3116, which is consistent with the previous report. In addition to auxin, the TaIAA1 gene is also induced by brassinosteroids. Several genes showed accessionspecific expression profile, such as the 51 and 41 gene sets, which may reflect differences in anatomical features and the plant’s response to its immediate environment. For instance, the levels of transcripts homologous to rice germin-like protein 1 show decrease in DV92 but increase in G3116 in lightexposed seedlings. The germin-like protein-1 in rice has been shown to play a role in the regulation of plant height and disease resistance. Transcripts homologous to genes coding for heat shock protein 90 and cpn60 chaperonin family protein increase in DV92, but decrease in G3116 in response to light. Changes in the expression levels of transcripts encoding components of hormone biosynthesis, signaling and protein targets suggest that photomorphogenesis is a carefully orchestrated interplay of both developmental signals and light response. We identified over 500,000 SNP sites and approximately 22,000 SSR/microsatellite sites in the transcriptome assemblies of T. monococcum. Of these, 9,808 SNP and 148 SSR sites are common polymorphic sites in both accessions. The 9,808 SNPs overlap 2,543 barley genes that show light mediated up and downregulation of homologous transcripts in T. monococcum. A few notable genes in this differentially expressed set include the light down-regulated protein coding genes for CASP-like membrane protein, Xyloglucan endo-transglycosylase activity, Auxin-responsive family protein and a novel protein carrying the DUF1644 domain. Whereas, the light up-regulated protein coding genes includes, photosystem-I subunit PSAK, PSAH, Ribulose-1,5-bisphosphate carboxylase small subunit RBCS, Chlorophyll a/b binding protein LHCB.