Protein is a major potential source of raw materials for new drugs. In this study, protein isolation of the red algae, Eucheuma cottonii was performed using a polar solvent (0.1 M Tris-HCl buffer). Purification of protein used fractionation method with ammonium sulfate, and then the last step of the isolation process performed protein dialysis. Determination of protein content was done using the Lowry method. Antibacterial activity test used agar diffusion method while for screening anticancer activity used the Brine Shrimp Lethality Test (BSLT) method. Anticancer effectiveness carried out against HeLa cancer cells. The results of antibacterial and BSLT tests on protein fractions F1 (0-20%) and F2 (20-40%) showed that these fractions were potential as anticancer agents, However, the test results of both fractions against HeLa cancer cells showed only the F2 protein fraction (20-40% fraction) was active in inhibiting the growth of HeLa cell cancer in the moderate category. The SDS PAGE electrophoresis test showed that the F2 protein fraction had a molecular weight of 26,76 kDa.