Low-carbohydrate, high-fat diets enhance lipid metabolism and decrease reliance on glucose oxidation in athletes, but the associated gene expression patterns remain unclear. The purpose of this study was to determine whether coordinated molecular pathways in skeletal muscle may be revealed by differential expression of genes driven by dietary profile, exercise, and/or their interaction. We investigated the skeletal muscle transcriptome in elite ultra-endurance athletes habitually (~ 20 months) consuming a high-carbohydrate, low-fat (HC, n = 10, 33 ± 6y, VO2max = 63.4 ± 6.2 mL O2•kg-1•min-1) or low-carbohydrate, high-fat (LC, n = 10, 34 ± 7y, VO2max = 64.7 ± 3.7 mL O2•kg-1•min-1) diet. Skeletal muscle gene expression was measured at baseline (BL), immediately-post (H0), and 2 h (H2) after 3 h submaximal treadmill running. Diet induced a coordinated but divergent expression pattern at BL where LC had higher expression of genes associated with lipid metabolism. Exercise resulted in a dynamic but uniform gene response, with no major differences between groups (H0). At H2, gene expression patterns were associated with differential pathway activity, including inflammation/immunity, suggesting a diet-specific influence on early muscle recovery. These results indicate that low-carbohydrate, high-fat diets lead to differences in resting and exercise-induced skeletal muscle gene expression patterns, underlying our previous findings of differential fuel utilization in elite ultra-endurance athletes.