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Abstract Objective Haemophilus haemolyticus can be misidentified as nontypeable Haemophilus influenzae (NTHi) due to their phenotypic similarities in microbiological culture. This study aimed to determine the prevalence of misidentified NTHi in respiratory specimens from children living in northern Australia. Results Among respiratory specimens collected in studies between 2010 and 2013, retrospective PCR analysis found that routine culture misidentified H. haemolyticus as NTHi in 0.3% (3/879) of nasal specimens, 25% (14/55) of bronchoalveolar lavage and 40% (12/30) of throat specimens. Therefore, in this population, PCR-based NTHi diagnostics are indicated for throat and bronchoalveolar specimens, but not for nasal specimens.