Carbon-based nanomaterials play central roles in both natural systems and emerging sustainable technologies, serving diverse functions from photoprotection in living organisms to energy harvesting and storage. Eumelanin, the brown-black melanin pigment, and natural organic matter (NOM), a similarly colored substance formed from the decomposition of biological material, represent two of the most widespread yet structurally elusive carbon-based materials in nature. Here, we present a detailed steady-state and time-resolved spectroscopic study, which reveals deep similarities in their photophysical properties as a consequence of common structural motifs at the nanoscale. While eumelanin and NOM have been traditionally studied independently and interpreted using molecular models, we introduce a framework centered on interchromophoric couplings to explain how common photoproperties emerge despite differences in their atomistic structures. By disassembling hierarchically structured eumelanin nanoparticles, we identify the fundamental spectroscopic units to be -stacked aggregates consisting of only a few layers. Our model explains how common photoproperties including transient spectral hole burning and excitation-wavelength-dependent emission arise from the ensemble behavior of these units. Our findings underscore the importance of focusing on how properties evolve through different levels of hierarchical assembly and provide a foundation for a unified photophysical framework that spans natural and lab-made carbon-based nanomaterials.