We did a comparative analysis between DNA-based subtypes and antimicrobial susceptibility profiles on Haemophilus influenzae and Haemophilus parainfluenzae, isolated from multiple tonsillar sites per individual from patients with chronic recurrent tonsillitis and/or tonsillar idiopathic hypertrophy and undergoing tonsillectomy and/or adenoidectomy. A total of eighty-eight Haemophilus isolates were obtained aseptically from the surface and core of tonsils and/or adenoids of 32 out of 60 patients and identified at the species level by the X and V factors and the API NH Kit. The H. influenzae and H. parainfluenzae isolates as well as ATCC strains were tested for antimicrobial susceptibility using a panel of antimicrobial agents. Random amplified polymorphic DNA (RAPD) was done on extracted DNA from all Haemophilus isolates and ATCC strains, using one 10 mer and one 18 mer primers to subtype the two species. Antimicrobial susceptibility testing data have shown a variation in generated susceptibility patterns to tested antimicrobial agents among H. influenzae and H. parainfluenzae isolates. This variation was demonstrated too among isolates obtained from different tonsillar sites (core and surface) in a single patient. RAPD analysis identified 58/88 (66%) different RAPD patterns. Variations in RAPD patterns among H. influenzae and H. parainfluenzae were also observed in isolates obtained from different tonsillar sites of the same individual. A correlation between RAPD patterns and antimicrobial susceptibility data, have shown: 1) the predominance of one strain (RAPD pattern) of either Haemophilus species among isolated organisms per patient, and exhibiting different antimicrobial susceptibility profiles or 2) the existence of multiple strains (RAPD patterns) of either Haemophilis species per patient, and showing either a single or multiple antimicrobial susceptibility profile(s). These observations question the validity of swab cultures obtained from a single tonsillar site per patient, for detection, identification and determination of antimicrobial profiles of the etiology of tonsillitis, since swab specimens taken from only one site may or may not reflect the etiology of infection.