Aims: The fungus Meira geulakonigii has been shown to reduce populations of citrus rust mite (CRM; Phyllocoptruta oleivora) on citrus leaves and fruits, in both the field and laboratory. However, attempts to isolate the fungus from leaves and fruits have been unsuccessful. The aims of this study were therefore to determine whether M. geulakonigii is a citrus endophyte, and to assess possible mechanisms involved in its mite-antagonist activity. Methods and Results: A quantitative real-time PCR and regular PCR approaches were developed to detect M. geulakonigii in both the field and laboratory. The fungus was detected throughout. Different methods revealed that M. geulakonigii is an endophyte, which colonizes both the peel of grapefruits. Applications of conidia protected the grapefruits against CRM, and fungal secretions extracted from growth media caused 100% CRM mortality. Conclusions: Meira geulakonigii is a beneficial endophyte of grapefruits that colonizes the fruit's peel, and protects it from CRM. Significance and Impact of the Study: Findings from this study demonstrate the endophytic nature of M. geulakonigii in its interaction with grapefruits. In addition, a molecular approach was developed to specifically detect the fungus inside the grapefruit peel. This approach can be used to assess the natural occurrence of M. geulakonigii in grapefruit.