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To advance our understanding of the molecular biochemistry of fungi which impact cultural heritage in libraries, museums and archives we investigated the diagnostic capacity of Raman spectroscopy to identify the composition of colored chromophores of fungi on paper. In this study we explored the diagnostic capacity of resonant Raman to distinguish chromophores in fungal filaments stimulated to grow on paper under high humidity with a focus on characterizing chromophores of Alternaria group species. To facilitate molecular analysis, we conducted quantum chemistry calculations of representative metabolites having optical absorption in the ultraviolet–visible spectral range. Comparing theory and experiment we show that fonsecin, erythroglaucin and aurasperone type chromophores occur in mature hyphal filaments with β-carotene dominant in yeast depositions on paper surfaces. Resonant Raman of mature filaments suggests a further contribution of carotenes longer than β-carotene to the spectral signature. Using microscopic resolution, we distinguish rich sets of Raman signatures that we assign to lignin, flavoglaucin, riboflavin, cycloleucomelon(e) and asperyellone molecular components in the spatial regions where filaments initiate from yeast depositions. In such regions, where filament microstructures stimulate development of a mature three-dimensional scaffold, the diversity of Raman resonances confirms a rich biochemistry of the developing structures. The library of computed optical and spectroscopic responses of characteristic fungal chromophores and metabolites presented here is essential for understanding the effect of fungi on a wide range of objects made from paper including books, prints, drawings, watercolors, engravings and even sculptures as well as designing next generation materials based on fungal hyphal mats. • Non-invasive Raman spectroscopy can be used to identify pigments in fungi. • Quantum chemistry (DFT) combined with Raman for quantitative measure of chromophores. • Computed optical responses of fungal chromophores and metabolites. • Raman spectroscopy combined with Quantum chemistry as tools for cultural heritage. • Alternaria sp. generates specific pigments when grown on paper. [ABSTRACT FROM AUTHOR]