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Estimating alpha-diversity and species distributions provides baseline information to understand factors such as biodiversity loss and erosion of ecosystem services. Yet, species surveys typically cover a small portion of any country's landmass. Public, global databases could help, but contain biases. Thus, the magnitude of bias should be identified and ameliorated, the value of integration determined, and application to current policy issues illustrated. The ideal integrative approach should be powerful, flexible, efficient, and conceptually straightforward. We estimated distributions for >6,000 species, integrating species sightings (S) from the Global Biodiversity information Facility (GRIF), systematic survey data (S-2), and "bias-adjustment kernels" (BaK) using spatial and species trait databases (S-2 BaK). We validated our approach using both locational and species holdout sets, and then applied our predictive model to Panama. Using sightings alone (the most common approach) discriminated relative probabilities of occurrences well (area under the curve [AUC] = 0.88), but underestimated actual probabilities by similar to 4,000%, while using survey data alone omitted over three-quarters of the >6,000 species. Comparatively, S-2 BaK had no systematic underestimation, and substantially stronger discrimination (AUC = 0.96) and predictive power (deviance explained 47%). Our model suggested high diversity ( similar to 200% countrywide mean) where urban development is projected to occur (the Panama Canal watershed) and also suggested this is not due to higher sampling intensity. However, portions of the Caribbean coast and eastern Panama (the Darien Gap) were even higher, both for total plant biodiversity (similar to 250% countrywide mean), and CITES listed species. Finally, indigenous territories appeared half as diverse as other regions, based on survey observations. However, our model suggested this was largely due to site selection, and that richness in and out of indigenous territories was roughly equal. In brief, we provide arguably the best estimate of countrywide plant alpha-diversity and species distributions in the Neotropics, and make >6,000 species distributions available. We identify regions of overlap between development and high biodiversity, and improve interpretation of biodiversity patterns, including for policy-relevant CITES species, and locations with limited access (i.c., indigenous territories). We derive a powerful, flexible, efficient and simple estimation approach for biodiversity science.