The present study aimed to investigate the powerfulness of the two microsatellite panels (ISAG against TKY) for genetic characterization and parentage assignment of closely related Arabian horse families. A total of 41 Egyptian Arabian horse samples representing eight sire families were analyzed by two panels (12 markers of ISAG against 12 markers of TKY). The basic measurements of genetic diversity and parentage were estimated. The TKY panel showed higher genetic diversity parameters (Na = 6.250; Ne = 3.33; HO = 0.655; HE = 0.691; PIC = 0.6335) than ISAG Panel (Na = 5.000; Ne = 2.994; HO = 0.646; HE = 0.657; PIC = 0.601). The parentage assignment of the eight sire families by using the two panels was successfully indicated by their higher power of exclusion 0.99999 and 0.99998, for TKY and ISAG panels, respectively. TKY panel will continue to be an additional and confirmatory panel in single system exclusion within the ISAG panel. Cervus software provided an accurate and rapid method in the assignment of Arabian horse parentage.