The carriage ofCandida albicansin children’s oral cavities is associated with a higher risk for early childhood caries, so controlling this fungus in early life is essential for preventing caries. In a prospective cohort of 41 mothers and their children from 0 to 2 years of age, this study addressed four main objectives: (1) Evaluate in vitro the antifungal agent susceptibility of oralCandidaisolates from the mother-child cohort; (2) compareCandidasusceptibility between isolates from the mothers and children; (3) assess longitudinal changes in the susceptibility of the isolates collected between 0 and 2 years; and (4) detect mutations inC. albicansantifungal resistance genes. Susceptibility to antifungal medications was tested by in vitro broth microdilution and expressed as the minimal inhibitory concentration (MIC).C. albicansclinical isolates were sequenced by whole genome sequencing, and the genes related to antifungal resistance,ERG3,ERG11,CDR1,CDR2,MDR1, andFKS1, were assessed. FourCandidaspp. (n = 126) were isolated:C. albicans, C. parapsilosis, C. dubliniensis, andC. lusitaniae. Caspofungin was the most active drug for oralCandida, followed by fluconazole and nystatin. Two missense mutations in theCDR2gene were shared amongC. albicansisolates resistant to nystatin. Most of the children’sC. albicansisolates had MIC values similar to those from their mothers, and 70% remained stable on antifungal medications from 0 to 2 years. For caspofungin, 29% of the children’s isolates showed an increase in MIC values from 0 to 2 years. Results of the longitudinal cohort indicated that clinically used oral nystatin was ineffective in reducing the carriage ofC. albicansin children; novel antifungal regimens in infants are needed for better oral yeast control.