Better management of soils for grape and wine production will deliver broad ranging benefits. Here we describe an important, largely unquantified feature of four Australian wine growing soils, the soil microbial community, using medium and high resolution DNA-based approaches (TRFLP and amplicon sequencing of 16SrRNA and ITS). The significance of these microbial communities relates to their dual roles in soil health and wine quality. To address soil health, we explore the use of sequence-based microbial metrics such as bacterial and fungal diversity in soils of 4 economically significant wine growing regions (e.g. Barossa, McLaren Vale, Sunraysia and Yarra Valley). We compared location in vineyards (eg Undervine and Mid-Row) and accessed an adjacent Non-Vineyard site. These metrics were assessed against accepted chemical and biological standards of soil health. These agreed measures represent the minimum data set (mds) recommended for assessing soil health in vineyards. The medium resolution technology (e.g. TRFLP 16S & ITS) indicated that bacterial and fungal communities differ in composition with respect to regional (e.g. Barossa, McLaren Vale, Sunraysia and Yarra Valley) and locational factors (mid-vine, under-vine and adjacent native vegetation). Both TRFLP and amplicon sequencing of 16SrRNA and ITS methods generated OTU and taxa that indicated strong regional community clusters for the Yarra Valley and Sunraysia that could be correlated strongly to soil pH (and interrelated measures such as Ex Ca and CaCO3) and organic and labile C and N. Similarly for both techniques, vineyard locational differences in communities were greatest between the undervine and non-vineyard sites with the mid-row location being intermediate and influenced by chemical characteristics that comprise the mds for soil health. Biodiversity metrics generated from TRFLP and amplicon sequencing of 16SrRNA and ITS differentiated regionally and locationally but these data could not be strongly related to the chemistry mds for soil health. An argument is presented for incorporating improved metrics in an mds for soil health in vineyards.