Children’s oral health is in a dire state, with dental decay (caries) being one of the most common chronic diseases. While the pivotal role of bacteria in the oral microbiome and its contribution to dental caries is established, the contribution of fungi is relatively unknown. The increased abundance of the fungi, Candida albicans, is suggested to contribute to caries development. We assessed the oral mycobiome makeup in childhood (n = 17), to determine if the composition of fungi varies between children with and without caries. Oral mycobiome composition was assessed by amplifying the ITS2 region from supragingival dental plaque DNA extracts and sequencing these amplicons with Illumina MiSeq. This revealed that the oral mycobiome in the investigated children contained 46 fungal species from three phyla (Ascomycota, Basidiomycota and Zygomycota). Candida albicans was the most abundant species and was ubiquitous in all samples regardless of whether caries was present. While the overall diversity of fungi was similar, independent of whether caries was present (p > 0.05), we found that caries influenced the abundance of specific fungi. Children with healthy teeth had a significantly higher abundance of 17 species compared to children with caries, who had only three enriched species (p < 0.001). The ubiquity and dominance of Candida albicans in the oral microbiome of children with and without caries indicates this species may not be involved in caries development. While the species found to be differentially abundant between health and caries may be specific to an Australian population, our findings indicate fungi in the oral microbiome potentially influence oral health. Resolution of the aetiology of caries requires analysis of both fungal and bacterial communities in the oral microbiome.