In order to enrich the ovine genome and provide a basis for future molecular genetics and functional genomics analyses in sheep, we used de novo assembly to establish transcriptomes of skeletal muscle tissues of Dorper and Small-tailed Han sheep. A total of 103,058,824 clean Illumina paired-end sequencing reads from the two libraries were assembled into 145,524 unigenes in a de novo project. There were 5718 unigenes showing differential expression between the two transcriptomes, and 7437 coding SSRs were exploited. After further assembly, we identified a total of 70,348 all-unigenes with an average length of 863 bp; 35,201 of these all-unigenes could be annotated in the Nr database, and 12,219 were found in the clusters of orthologous groups database. Gene ontology searches indicated cell and binding as the main terms. Among 258 Kyoto Encyclopedia of Genes and Genomes database pathways, protein and amino acid metabolism pathways were the most commonly identified. We analyzed the ovine muscle transcriptome using high-throughput sequencing technology. Many unigenes were assembled and numerous molecular markers and differential expressed unigenes were identified.