Soil microorganisms are important in global nutrient cycling and organic matter decomposition. Yet, our knowledge of soil microbial community composition, especially in the tropics, is largely lacking. Anthrosols in the Brazilian Amazon, developed between 500 and 6,500 years before present by indigenous pre-Colombian Indians, are typically highly fertile and contain both archeological artifacts and charcoal. We characterized and compared microbial communities in four anthrosols with those in their paired adjacent, unmodified soils. The soils were collected from sites within the central Amazon basin and bacterial, archaeal and fungal communities characterized using two DNA fingerprinting techniques (DGGE and T-RFLP). We isolated and identified fungi cultured on media made from anthrosol extracts, and counted arbuscular mycorrhizal fungi (AMF) spores for each soil type. Our most striking findings were that the anthrosol microbial communities were similar to each other, regardless of distance between sites or vegetation cover; and that these communities were distinct from those in their respective adjacent soils. Sequencing of taxa unique to particular samples showed that both anthrosols and adjacent soils contain organisms that are taxonomically distinct from those found in sequence databases. We also found that AMF spore counts were significantly higher in anthrosols compared to adjacent soils. As we slowly unravel the biological mysteries of these soils, the data we generate are helping us to understand how specific soil management practices could support sustainable agriculture on highly weathered tropical soils, while at the same time giving us a window into indigenous soil management practices of the past.