Intraspecific variation is the collective genotypic and phenotypic variability among individuals and populations of a species. Its documentation across taxa is considered essential for understanding ecological-evolutionary processes and biodiversity consequences in Anthropocene environments. The systematic assessment of intraspecific variation is, however, a complex task. Here, we present a conceptual approach for holistic surveying of intraspecific variation. We illustrate its feasibility through application in chimpanzees, a taxon with high anthropological significance for understanding hominid diversification and conservation importance as flagship and umbrella species. By establishing a large-scale, highly collaborative and well-structured network of research sites, standardized genomic, microbiome, mycobiome, physiological, dietary, demographic, behavioral and ecological data could be collected across many populations. Studies unprecedented in scale, complexity, and disciplinary integration allow addressing long-standing questions and complex topics which previously could not be studied with existing approaches restricted in extent and scale. Adopting similar approaches for other taxa exhibiting high intraspecific variation, including other primates, corvids, parrots or cetaceans will advance holistic species understanding. Such work will reveal generalizable patterns and improve understanding of contexts shaping ecological-evolutionary processes underlying the emergence of intraspecific variation, facilitating inclusion of intraspecific variation into conservation strategies and revealing consequences of losing intraspecific variation in Anthropocene environments.