Fungi are a known cause of mastitis in cattle. Despite this, fungal milk communities associated with development of intramammary infections are under researched. Mastitis is one of the most common and costly diseases in dairying, particularly due to decreased production in subclinical cases. Commonly, broad-spectrum antibiotics are used in treatment and may lead to an unbalanced milk microbial community (microbiome), potentially allowing for overgrowth of mastitis-causing fungi. This research aims to explore the microbiome associated with healthy and mastitic (clinical and subclinical) milk, with a focus on fungi and bacterial-fungi interactions, and implications of repeated antibiotic usage. This work will contribute to a knowledge gap in dairying, by i) identifying potential milk microbiome biomarkers relating to health status, ii) providing evidence for pre/probiotic development, iii) exploring whether repeated antibiotic usage impacts upon microbiome communities and reoccurrence of mastitis. This knowledge could help farmers and industry in tackling a global issue.