We previously reported that both maternal under- and over-feeding altered muscle cross sectional area and lipid content in offspring. Therefore, we hypothesized that poor maternal nutrition would alter key pathways and novel genes involved in muscle development of lambs. Ewes (n = 3/treatment) were fed 100% (CON), 60% (RES), or 140% (OVER) of NRC requirements for TDN and one twin lamb per ewe was euthanized within 24 h of birth and muscle tissue was collected for RNA-Seq analysis. RNA was prepared into cDNA libraries and sequenced using the Ion Torrent Proton. Data were aligned to the Bos taurus (Btau_4.61) and Ovis aries (Oar_V.3.1) reference genomes using Tophat and expression evaluated with Cufflinks. Differential gene expression was determined using the Benjamini-Hochberg multiple testing correction (q ≤ 0.05). Using the ovine and bovine references, 10 and 35 differentially expressed genes were identified, respectively. The differentially expressed genes are involved in metabolic regulation, hypertrophy, nutrient uptake, and protein turnover. Using the ovine reference, compared with CON, expression of myogenic factor 6, and myostatin increased 1.7 and 2.0-fold in OVER (q ≤ 0.05). BTG family member 2, ankyrin repeat domain 1, and phosphoserine phosphatase expression decreased 1.5, 2.5, and 3.1-fold, respectively in OVER (q ≤ 0.05). Expression of FHJ murine osteosarcoma viral oncogene homolog (FOS) was reduced 1.6-fold in RES compared with CON (q = 0.05). Using the bovine annotation, compared with CON, arrestin domain containing 2 and AT rich interactive domain 5B expression were 3.5 and 2.9-fold greater, respectively in OVER (q = 0.05). Expression of PPARγ coactivator 1 α, regulator of G-protein signaling 16, thrombomodulin, and jun B proto-oncogene were reduced ≥2-fold (q ≤ 0.05) in OVER. Tripartit motif containing 63, FOS and suppressor of cytokine signal 3 expression were reduced 1.4, 1.6, and 2.8-fold, respectively in RES (q ≤ 0.05). In conclusion, although both under- and over-feeding had similar effects on offspring muscle development, based on gene expression, the mechanisms through which this occurs appear to be different.