Grapevines that are used for winemaking host a diverse range of microorganisms that make up their microbiome. The microbes that inhabit the grapevine have been used by winemakers to produce wine for centuries, although modern wine producers often rely on inoculated microorganisms such as Saccharomyces cerevisiae. In the Australian wine industry, there is a movement towards returning to the utilisation of the microbiome for wine fermentation. With the recent increase in the understanding of the role of the grapevine microbiome in grapevine health, fermentation and subsequent wine sensory traits, the microbial world offers a new level of complexity that can be harnessed for winemaking. In order to develop and maintain a desired vineyard micro-biodiversity, extensive microbial monitoring is required. Here we discuss the utilisation of a viability selection dye in order to distinguish between microorganisms that are live and associated with the host, and relic signals generated from non-living sources.