Johne's disease (JD) caused by Mycobacterium avium subsp. paratuberculosis (MAP) represents a real threat to the agriculture and dairy food industries and believed to be a potential public health problem. No treatment for the disease exists and controlling the disease is difficult due to its long latent period. This study aimed to evaluate two diagnostic methods culture and PCR assay for detection of MAP in feces under the Egyptian circumstances. A total 200 fecal samples were collected from dairy cattle showed chronic diarrhea and have history of Johne's infection. Fecal culturing revealed 87 (43.5 %) positive from the total collected samples. In another side, the PCR targeting IS1311 revealed that 94 (47%) out of 200 of examined cattle were positive for MAP. Consequently, the both tests showed good agreement between them (Kappa value = 0.869). The sequence analysis of the obtained isolate showed that the Egyptian isolates (LC428286 and LC428285) have high similarity with MAP strain JII-1961 from Germany and MAP 316V strain of Netherlands reach up to 98%.