Enterobacter agglomerans (Pantoea Agglomerans) and Klebsiella pneumonia are opportunistic Enterobacteriaceae, lactose fermenting and a Gram-negative rod. It is apprised as commensal pathogens of animal and human. Isolation and identification of Enterobacter agglomerans (Pantoea Agglomerans) and Klebsiella pneumoniae from aborted mares were depended on the characters and features of colonies on blood agar plate and McConkey agar plates in addition to biochemical tests to isolated colonies from aborted cases according to Microbact™ Gram-negative system. Five mares have been aborted. Pure colonies of Enterobacter agglomerans (Pantoea Agglomerans) were isolated from two mares while pure colonies of Klebsiella pneumonia were isolated from one mare. Mixed infection of Enterobacter agglomerans (Pantoea Agglomerans), Klebsiella pneumoniae, Escherichia coli and Citrobacter spp. was isolated from two-aborted mare. Abortion rate in mares was 5.9 % (5/85). Isolated colonies of Enterobacter agglomerans (Pantoea Agglomerans) were susceptible to Ciprofloxacin (CIP) (100%) whilst Isolated colonies of Klebsiella pneumonia were susceptible to Ceftriaxone (CRO) (100%). Both of two species were resistant to Ampicillin (AMP), Gentamicin (CN) and Tetracycline (TE). The isolation of Enterobacter agglomerans (Pantoea Agglomerans) and Klebsiella pneumoniae from vaginal cervico swabs after mare’s abortion suggests them to be a cause of abortion in mares.