Significance Our study shows that deep subseafloor sediments are populated by descendants of rare members of surface sediment microbial communities that become predominant during burial over thousands of years. We provide estimates of mutation rates and strength of purifying selection in a set of taxonomically diverse microbial populations in marine sediments and show that their genetic diversification is minimal during burial. Our data suggest that the ability of subseafloor microbes to subsist in the energy-deprived deep biosphere is not acquired during burial but that these microbes were already capable of living in this unique environment. These findings represent a significant step toward understanding the bounds for life in the deep biosphere and its connection to life in the surface world.