Fast skeletal troponin C (TNNC2) plays a key role in the regulation of muscle contraction, and modulates the Ca2+-activation characteristics of muscle fibers. In this study, we characterized the full-length cDNA of the porcine TNNC2 gene, which is composed of a 65 bp 5'UTR, a 483 bp (ORF) and a 174 bp 3' UTR. Northern blot analysis indicated that the TNNC2 gene had one transcript of approximately 0.7 kb and was expressed exclusively in skeletal muscle (triceps brachii, biceps femoris and longissimus dorsi). SDS-PAGE and Western blotting analysis indicated that the porcine TNNC2 protein comprised 160 amino acids, and had a molecular mass of 18 kDa. The porcine TNNC2 gene, which spans 3.2 kb, was isolated and was found to be composed of six exons. All exon/intron boundaries adhered to the GT/AG rule. Altogether 20 nucleotide polymorphisms of the TNNC2 gene were discovered in Duroc, Landrace, Lantang and Dahuabai pigs, and included three missense mutations and 17 intronic substitutions. Five of the polymorphisms were genotyped in Lantang, Dahuabai, Landrace, Large White and Duroc pigs using PCR-RFLP. Significant differences in genotype frequencies were observed between the Chinese native breeds (Lantang and Dahuabai) and the western breeds (Landrace, Large White and Duroc). These datas have identified the TNNC2 gene as an excellent model system for studies of developmentally regulated gene expression and a novel marker suitable for studies of the association of candidate genes with growth traits in porcine skeletal muscle.