The present investigation was done to define the identity of six maize inbred lines using SDS-PAGE protein analysis and some isozymes variability, DNA fingerprinting detected by inter simple sequence repeat (ISSR)-PCR molecular markers. Protein electrophoresis revealed that total number of bands ranged from 12 in the inbred line Sids 1108 to 4 in inbred line Sids 1157 and inbred line Sids 63. Three common bands were found in all tested inbred lines. Two inbred lines; Sids 7 and Sids 1108 showed specific bands which could be used to distinguish them from the others. In addition, bands of two isozymes systems, peroxidase (Prx) and esterase (EST) were determined for the six maize inbred lines based on polyacrylamide gel electrophoresis. The number of bands and R_f values could be used to identify these inbred lines. Eleveen anchored ISSR primers were used for fingerprinting of the six maize inbred lines and obtained 73 scorable bands, 42 of them were polymorphic (58 %). Sids 7 produced two bands with two primers (ISSR 1and ISSR 10). Sids 34 produced three bands with three primers (ISSR 1, ISSR 9 and ISSR 11). Sids 1159 produced three bands with three primers (ISSR 2, ISSR3 and ISSR 8). Sids 1108 produced two bands with two primers (ISSR 6 and ISSR 7). Sids 1157 have one band marker with primer ISSR 11. Also, Sids 63 has one band marker with primer ISSR 3. Existing genetic differences between inbred lines are important from the point of view of the breeder to take advantage in maize improvement programs.