Protein recovery under sonication treatment and autolysis, also protein hydrolysis progress during enzymatic hydrolysis (using trypsin and chymotrypsin) and autolysis (using endogenous enzymes) were investigated in Saccharomyces cerevisiae and Kluyveromyces marxianus. Crude protein content of dried yeast cells were 53.22% and 45.6% for S.cerevisiae and K.marxianus, respectively. After 96 hrs of autolysis in the presence of ethyl acetate, protein recovery reached 59.74% and 77.18% for S. cerevisiae and K. marxianus, respectively and it was 53.66% and 55.17% for sonication treatment. The yeast protein solution obtained by sonication was hydrolyzed by trypsin and chymotrypsin.  Autolysis, produced hydrolysates with higher degree of hydrolysis (DH) values as compared to the enzymatic hydrolysis. After 96 hours autolysis, DH increased to 48.75% and 39.51% for S. cerevisiae and K. marxianus respectively. Chymotrypsin was significantly more effective on K. marxianus protein with the DH value of 21.59%, but the effect of trypsin was the same in the two yeast strains (DH value of 18.5%). It can be concluded that the autolysis process is significantly more effective than enzymatic hydrolysis by producing smaller peptides