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Background: Fungal sepsis in neonates is still one of the major causes of morbidity and mortality despite advances in health care. This study aimed to characterize fungal agents of sepsis in neonates and their susceptibility pattern. Methods: This was a cross-sectional study among neonates in two tertiary health care facilities in Jos. Neonates with sepsis whose parents consented to the study were recruited based on the Integrated Management of Childhood Illnesses(IMCI) criteria. Blood sample was collected for culture, antifungal susceptibility test and molecular characterization of fungal agents isolated from blood culture of the neonates was performed using the ribosomal DNA (rDNA) of the internal transcribed spacer (ITS) region. Univariate and bivariate analysis was carried out using STATA statistical software (version 14 IC). Results: The prevalence of fungal sepsis in neonates was 5.5%. Candida albicans was responsible for 11 of the 20 cases of neonatal fungal sepsis. All the fungal isolates were susceptible to the antifungal agents used except for a little resistance by C. glabrata observed to amphotericin B (%R=0.3). Bayesian analysis confirmed the major phylogenetic relationships among the isolates and molecular identification of the different Candida species. Conclusion: Candida albicans are the major cause of neonatal fungal sepsis. The study highlights the need to evaluate the causes of neonatal fungal sepsis, their antifungal susceptibility pattern and molecular characterization for early implementation of medical intervention to reduce the morbidity and mortality.