Candidemia is a leading cause of sickness and mortality in neonatal care. Although current diagnostic methods are beneficial, a better knowledge of molecular pathways is necessary for enhancing detection. This study used molecular techniques to assess the incidence of candidemia in infants being treated in Iraqi NICUs. Using a cross-sectional experimental design, blood samples from newborns exposed to different risk factors were analyzed. The use of polymerase chain reaction (PCR) that targeted the ITS1 and ITS2 regions facilitated the identification of fungi. Several Cladosporium species, such as Cladosporium macrocarpum, Cladosporium allicinum, Cladosporium limoniforme, Cladosporioides, and Cladosporium tenuissimum, were found, which was unexpected. A phylogenetic study indicated the widespread distribution of these strains throughout Asia and North America. Cladosporium's unexpected appearance necessitates a broadening of infection control measures and diagnostic perspectives in healthcare facilities. The findings of this research stress the need for constant vigilance and an all-encompassing approach to infection and diagnosis management in NICUs.