Background: The opportunistic pathogen Klebsiella pneumoniae is one of the main causes of pediatric bacterial blood stream infections (BSI), which is complicated with sepsis and high mortality. Objectives: To identify atypical Klebsiella species affecting a sample of infected neonates with low antimicrobial response. Methods: Multidrug resistant blood cultures for Klebsiella from a Neonatal Service, were submitted to molecular identification by sequencing analysis of 16S ribosomal RNA. Results: The mean age of the newborns was 14.7 ± 5.6 days. A total of 6 out of 8 cases were sepsis, 1 case of pneumonia, and 1 a catheter-related infection. The molecular identification showed 3 cases of K. pneumoniae subsp. ozaenae, 2 of K. pneumoniae and K. variicola, and 1 case of K. oxytoca. The highest antimicrobial resistance was against cephalosporins and Trimethoprim/sulfamethoxazole. Conclusions: Klebsiella pneumoniae subsp. ozaenae was responsible for multidrug resistant strains of Klebsiella even in 37.5% of cases. In our clinical setting, the use of Amikacin and carbapenems are still useful to treat neonatal infections by Klebsiella even against K. variicola, which is the most resistant.