Proteins in catfish by-products were extracted by two methods: Alkaline extraction (AE) and salt extraction (SE). Properties of the fish protein isolate (FPI) were measured by protein yield and content, moisture content, SDS-PAGE protein patterns, color and texture profile, and compared with commercial surimi products. Our results showed that catfish frame had higher protein yield and color similarity with commercial products than the head; AE-FPI had higher yield and gel strength than SE-FPI; SDS-PAGE protein patterns of FPI from catfish frame by SE method was comparable with commercial surimi products. Based on the results, further optimization of the recovery yield of protein extracted by alkaline extraction method, and effect of microbial transglutaminase (MTGase) on gelation properties under various concentration and reaction time was investigated. Results indicate that the protein yield reached up to 60%, and the addition of MTGase in protein isolate effectively improved the gel forming ability.