The objective of this study was to examine the effect of level and duration of feeding of an n-3 PUFA-enriched fish oil (FO) supplement in combination with soybean oil (SO) on the transcriptional regulation of Delta(9)-desaturase gene expression in bovine muscle. Beef bulls (n = 40) were assigned to 1 of 4 iso-lipid and isonitrogenous concentrate diets fed for ad libitum intake for a 100-d finishing period. Concentrates were supplemented with one of the following: 1) 6% SO (CON); 2) 6% SO + 1% FO (FO1); 3) 6% SO + 2% FO (FO2); or 4) 8% palmitic acid for the first 50 d and 6% SO + 2% FO for the second 50 d [FO2(50)]. Samples of LM were harvested and concentrations of fatty acids were measured. Total RNA was isolated and the gene expression of Delta(9)-desaturase was determined. The mRNA expression of putative regulators of Delta(9)-desaturase gene expression, sterol regulatory element binding protein-1c (SREBP-1c) and peroxisome proliferator activated receptor-alpha (PPAR-alpha), were also measured in the CON and FO2 groups. Expression of mRNA for Delta(9)-desaturase was decreased (P < 0.05) 2.6-, 4.4-, and 4.9-fold in FO1, FO2(50), and FO2 compared with CON, respectively. Expression of Delta(9)-desaturase mRNA tended to be reduced (P = 0.09) by increasing FO from 1 to 2%, but was not affected by duration of supplementation (P > 0.24). Expression of mRNA for SREBP-1c was decreased 2-fold in FO2 compared with CON (P < 0.05), whereas expression of PPAR-alpha was not affected (P > 0.30). There was a positive relationship between Delta(9)-desaturase and SREBP-1c gene expression (P < 0.01), but the expression of both genes was negatively related to tissue concentrations of n-3 PUFA (P < 0.05) and positively related to concentration of n-6 PUFA (P < 0.01). Simultaneous enhancement of tissue concentrations of CLA and n-3 PUFA concentrations in bovine muscle may be hindered by negative interactions between n-3 PUFA and Delta(9)-desaturase gene expression, possibly mediated through reduced expression of SREBP-1c.