The cave bat; Geoffroy's bat (Myotis emarginatus), is an important component of the animal life in Northern Iraq, which lives in huge numbers in the mountain caves of that region. These numbers when they fly hunting for food may cause spreading of some pathogenic microbes. Thus, the current study looked at identifying the presence of Pseudomonas aeruginosa in the intestine content of these bats. In this case, 55 bats were captured, and 45 intestinal swab samples were taken. These samples were examined by using cultivation and biochemical methods. The colonies were subjected to a PCR and sequencing by recruiting the 16S rRNA gene as a target. The sequencing data were processed for the identification of any evolution properties and displayed by presenting a phylogenetic tree. The cultivation and biochemical findings revealed the presence of the bacterium in 8/55 (14.6%) of the samples. These positive results were confirmed by using the PCR and found that 8/8 (100%) of the samples were positive for the pathogen. The sequencing and the phylogenetic analyses of three randomly selected PCR purified products revealed close similarity with global sequences isolated from human lung and animal food in the UK and Italy, respectively. The current results show important information about the possible pathogenicity of Pseudomonas aeruginosa present in the intestine of the examined bat, which may pose a real threat to the health of people who are in contact with these bats.