Objectives To identify the route and time of transmission by Candida species from mothers' vagina to their neonates' mouth.Methods Specimens for fungal cultures were obtained from vaginal discharge of mothers just before delivery and also from the mouth of their offspring just after birth.Eleven mother-infant pairs were investigated.Candida species was identified based on morphology,biochemical analysis,and sequencing of D1/D2 domain of the large subunit of ribosomal DNA (LSUrDNA).Electrophoretic karyotyping (EK) and random amplified polymorphic DNA analysis (RAPD) were performed to search for DNA homology.Results Candida isolates (16 strains) from 8 mother-infant pairs were identified as Candida albicans by 100% homology of their D1/D2 sequences with reference strain C.albicans Y-12983 (GenBank access No.U45776).Similarly,4 strains from two mother-infant pairs and 2 isolates from the other pair were identified as Candida glabrata and Candida krusei,respectively,by 100% homology in sequences alignment of the domains with reference strains,C.glabrata Y-65(U44808) and C.krusei Y-5396 (U76347).The same EK profiles were found for each C.albicans or C.krusei strain pair from both mother and her neonate.Although different EK bands with various molecular size were generated for each C.glabrata isolate pair,they were still considered to be homologous based on the fact that main EK bands were identical.Each isolate pair from mother and her infant presented almost the same RAPD profile,except for one pair,isolates F7n and F7m,which showed minor diverse DNA bands.Conclusion Eleven Candida isolates from neonates have identical molecular characteristics with their mother's isolates.Vertical transmission may be the main pathway of Candida spp.from mothers to their neonates.