The thermotolerant Bacillus associated with Bikalga and Soumbala process were screened numbered and identified using standards and PCR methods. Thermotolerant bacteria in Soumbala ranged from 1.35 x [10. sup. 9] to 3 x [10. sup. 9] cfu/g, 1.24 x [10. sup. 9] to 2.78 x [10. sup. 9] cfu/g, 0.54 x [10. sup. 9] to 2.27 x [10. sup. 9] cfu/g, 3.5 x [10. sup. 7] to 1.54 x [10. sup. 9] cfu/g respectively for 90 [degrees] C, 95 [degrees] C, 100 [degrees] C and 105 [degrees] C. Thermotolerant bacteria in Bikalga ranged from 1.9 x [10. sup. 7] to 12.8 x [10. sup. 7] cfu/g, 2x [10. sup. 6] to 11.2 x [10. sup. 7] cfu/g, 0 to 9.6 x [10. sup. 7] cfu/g, 0 to 7.6 x [10. sup. 7] cfu/g respectively for 90 [degrees] C, 95 [degrees] C, 100 [degrees] C and 105 [degrees] C. Sixteen strains were selected and identified as belonging to Bacillus genera. All these selected strains are Gram positive, catalase positive and endospore forming …