Intestinal and human milk microbiota studies during infancy have shown variations according to geographical location, delivery mode, gestational age, and mother-related factors during pregnancy. In this study, we performed metagenomic mycobiota analyses of 44 transient and mature human milk among five different groups: mothers of normal spontaneous delivery-term (NS-T), caesarean delivery-term (CS-T), premature (PT), small for gestational age (SGA), and large for gestational age (LGA) infants. Fungi were detected in 80 out of the 88 samples. Regarding the number of observed fungal species, the NS-T group was more homogeneous (less variable) comparing the other groups (P<0.05). In the transient human milk samples, the most abundant species were Saccharomyces cerevisiae (33.3%) and Aspergillus glaucus (27.4%). While A. glaucus (33.7%) was second most abundant species in mature milk, S. cerevisiae disappeared (P<0.01) and Penicillium rubens became the most abundant species (35.5%) (P<0.05). Among the NS-T group, the most abundant species was Malassezia globosa in both transient and mature milk. In contrast, S. cerevisiae was the most abundant species in transient human milk (45.0%) in the CS-T group, but it disappeared in mature milk (P<0.01). In transient milk, M. globosa was only represented 6.0-9.0% of taxa in the PT, SGA, and LGA groups (P<0.05). In transient and mature milk in the PT, SGA and LGA groups, the most abundant species were A. glaucus and P. rubens. In mature milk samples, P. rubens is more abundant in CS-T group, PT group and LGA group, than the NS-T groups (P<0.05 for all). Although fungi constitute only a very small part of the human milk microbiome, we observed some changes that the human milk mycobiota composition varies in caesarean delivery, premature, SGA and LGA groups, comparing the normal spontaneous delivery, as well as differences between transient and mature human milk.