Alpha and beta collagen subunits were isolated from golden pompano skins by cellulose column at different pH. As a result, the alpha(1) subunit and beta subunit were successively eluted by a linear gradient of 0-35 mM NaCl at pH 4.7, while alpha(2)-subunit was eluted at pH 5.2. SDS-PAGE result showed that the molecular weights of alpha(1), alpha(2) and beta subunits were about 131, 119 and 256 kDa, respectively. The contents of glycine, alanine and imino acids in the alpha(1) subunit were more similar to the beta subunit than alpha(2) subunit. Analyses of deduced amino acid sequences revealed that the theoretical sizes and isoelectric points of collagen alpha(1) were 137 kDa and pH 5.95, while those of collagen alpha(2) were 126 kDa and pH 9.27, respectively. Compared to the collagen alpha 2, collagen alpha(1) had a cysteine-rich domain, more tripeptide unit of Gly-Pro-Pro, and specific alpha-helix domain.