Problem Unexplained persistent or recurrent bacterial pharyngitis in some patients who suffer from infected middle ear cleft. Methods Bacteriological swabs were obtained from both the ears and the pharynx of 37 cases with chronic otorrhea and perforation, whom complain of recurrent or persistent sore-throat. Then isolation and identification of the micro-organisms were done. This included examination of direct Gram stained films and cultures. Isolated Gram negative bacilli were subjected to further identification by the biochemical reactions and antibiotyping. Identical isolates from the same patient (ear and pharyngeal swabs) were subjected to further identification by genotyping using the pulsed field gel electrophoresis technique. Results 6 cases (16%) showed identity in phenotypes and genotypes for ear and pharyngeal samples from the same patient. All pharyngeal isolates were Gram negative organisms. 4 of them were Pseudomonas aeruginosa, 1 was Proteus sp., and 1 was Escherichia coli. All of these 3 species are not known to be among the primary organisms which may cause pharyngitis. Conclusion Bacterial pharyngitis in patients with chronically infected middle ear cleft may be attributed to the same organism invaded the middle ear mucosa. Also this study highlights some organisms as a pharyngeal invaders although they are not among the previously documented causatives of bacterial pharyngitis. But the study do not confirm the method of spread of these organisms and whether this was directly via the eustachian tube. Significance The study correlates the causative organism of the middle ear infection and that infected the pharyngeal mucosa utilizing the advanced bacteriological identification and genotyping techniques.