Objective To explore the optimized condition for type differentiation of Mycobacteria strains and its value in applification by means of randomly amplified polymorphic DNA (RAPD) analysis. Methods RAPD condition for amplifying Mycobacteria DNA of clinically separated Mycobacteril strains from patients in Shenzhen was optimized, and then compared the features of RAPD electrophoresis strips. Results The best reaction condition for RAPD, taking stable, abundant and clear strips as criteria, were as the follows: in 50μl reaction system, there was 100ng template DNA, 2.5mmol/L MgCl_2,2U DNA polymerization enzyme, 0.5μmol/L primer and 250μmol/L of dATP、dGTP、dCTP and dTTP respectively; 40 reaction cycles, whose cycle procedure was: 94℃1min,36℃1min,72℃2min. At the above reaction conditions for RAPD, DNA of climically separated Mycobacteria strains were amplified, and the electrophoresis strips were abundant, clear, and evidently different from each other. Conclusion Mycobacterium tuberculosis and no-Mycobacterium tuberculosis can be differentiated by RAPD.