Focusing on the largely overlooked bioprospecting potential of diverse microbes colonizing seafloor massive sulphide (SMS) deposits, from active vent chimneys through to inactive, weathering mounds, we explore approaches for addressing potential use conflict between mineral and microbial resource exploitation. We are developing a ‘microbial landscape modelling’ methodology for the evaluation of SMS deposit-associated microbial genetic resources. Our small-scale pilot study on active sulphide edifices in the Main Endeavour vent field (Juan de Fuca Ridge, NE Pacific) is employing a remote-sensing approach that combines photogrammetric habitat reconstruction with microbial gene sequence data from samples collected from visually-distinct edifice habitats. We are using prokaryote 16S rRNA and micro-eukaryote 18S rRNA sequence data to ‘ground truth’ microbial diversity and genetic novelty to habitat features. We initially focussed on microbial assemblages associated with two common habitats colonized by the tubeworm Ridgeia piscesae: areas of high- and low-flow vent discharge. Our replicate sample data revealed a statistically robust distinction between flow regimes with respect to microbial diversity and genetic novelty. We then used the sequence data to assign scores for genetic diversity and novelty to microbes associated with the two tubeworm assemblages. Next, we will scale up this approach to enable landscape-scale comparison of the microbial resource potential of entire hydrothermal vent fields and extinct deposits. Developing comparative genetic resource maps for different deposit lifecycle stages: i. enables quantification of associated uncertainty and genetic resources loss resulting from mining deposits of various ages; ii. increases understanding of interactions between deposit weathering and biological processes.