Chlamydia abortus (C. abortus) is an obligate intracellular organism that undergoes a dimorphic life cycle within living cells. Little is known about Chlamydia abortus in rabbits. The objectives of this study were to detect C. abortus in domestic rabbits that were resident under desert conditions by quantitative species-specific real-time PCR (Polymerase Chain Reaction) Kit of C abortus 3-deoxy-D-manno-2-octulosonic acid transferase (kdtA) and by Giemsa staining. Samples were collected from 106 different samples from domestic desert rabbits including, North Sinai – Sahl El Tina (Coordinates:  31.0297°N 32.5658° E), South Sinai (Coordinates: 29.05°N 33.83°E), and the first point of Northwest Coast Amreya (Coordinates: 31.104538°N 29.766226°E), Egypt. Characteristic basophilic chlamydial inclusion bodies were detected in rabbit organs, In all feti and uteruses, 84.6% in intestines, 75% in the spleen, 69.2% in the lung, and 54.54% in the liver.Quantitative real-time PCR (qPCR) showed an exponential increase in C. abortus in organs and fecal samples. The significant incidence of C. abortus between organ and fecal samples in the Northwest Coast was assessed. C. abortus was detected in 88% of organs and 52% of fecal samples. On the other hand, C. abortus was recorded significantly among regions: 100% in North Sinai, 74.28% on the northwest coast, and 33.33% in South Sinai. Gabali Sinai and California were the most affected breeds. We concluded that the incidence of C. abortus became a reality in domestic rabbits under desert conditions. To our knowledge, this is considered the first molecular evidence of C. abortus in domestic desert Egyptian rabbits. Our results support the sustainable achievement in the newly reclaimed desert area of Sinai and the Northwest Coast. Attention should be given to newly disseminated Zoonotic and infectious microbes.