Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed pheno typic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome of nine lamb muscles: Semimembranosus(SM), Semitendinosus (ST), Cranial gluteobiceps, Gluteus medius (GM), Rectus femoris, Supraspinatus (SS), Longissimus lumborum (LL), Adductor and Psoas major. Significant gene expression differences were detected between almost all pairwise comparisons, being more pronounced between SS and ST, SM and LL, and ST and GM. These differences can be explained in terms of ATPase and glycolytic activities, muscle fiber typing and oxidative score, clustering muscles as fast glycolytic, intermediate or slow oxidative. ST showed up-regulation of gene pathways related to carbohy drate metabolism, energy generation and protein turnover as expected from a fast white muscle. SS showed myosin isoforms typical of slow muscles and high expression of genes related to calcium homeostasis and vascularization. SM, LL and GM showed in general intermediate gene expression patterns. Several novel transcripts were detected, mostly related to muscle contraction and structure, oxidative metabolism, lipid metabolism and protein phosphorylation. Expression profiles were consistent with previous histochemical and metabolic characterization of these muscles. Up-regulation of ion transport genes may account for significant differences in water holding capacity. High expression of genes related to cell adhesion, cytoskeleton organization, extracellular matrix components and protein phosphorylation may be related to meat yellowness and lower tenderness scores. Differential expression of genes related to glycolytic activity and lactic acid generation among fast, intermediate and slow muscles may explain the detected final meat pH differ ences. These results reveal new candidate genes associated with lamb meat quality, and give a deeper insight into the genetic architecture of these complex traits.