Stearoyl-CoA desaturase (SCD) plays a key role in lipid metabolism in humans and livestock. In ruminants, changes in the coding and/or regulatory sequences of the SCD gene could generate alterations in the enzymatic activity, producing variations in the fatty acid content in milk and meat. In this study, we investigated the genetic variability in 3989 bp of the ovine SCD gene. A total of 85 animals belonging to eight sheep breeds with different selection goals (dairy vs. meat) and fat metabolisms (fat-tailed vs. thin-tailed) were analysed. No polymorphisms were found within the coding region of the SCD gene (1080 bp). Analysis of the non-coding region (2909 bp) allowed the identification of four SNPs located in the promoter region (SCD01), intron 2 (SCD02 and SCD03) and intron 3 (SCD04). The most polymorphic SNP in the studied breeds was SCD01, which displayed intermediate frequencies in the highly specialised breeds, whereas it was less variable in the meat populations. Further efforts are needed to evaluate the potential use of the identified SNPs as markers for fat content and fatty acid composition of sheep products, and to assess the possible use of sheep as an animal model for human diseases related to lipid metabolism.