Closely related Aspergillus section Nigri species are difficult to resolve taxonomically, while short-read comparisons may be influenced by reference-genome choice. We applied reciprocal genome projection to 31 whole-genome sequencing libraries representing South African clinical section-Nigri isolates, Japanese and USA A. niger-labeled isolates, and A. welwitschiae-labeled isolates. Reads were aligned independently to A. niger ATCC 1015 and A. welwitschiae Aspwel1, followed by reference-specific differential-representation and KEGG analyses. Species-level classification showed substantial overlap between A. niger and A. welwitschiae. The A. welwitschiae–South African comparison identified 44 and 59 effect-qualified features under the respective projections, including 20 reciprocal feature pairs defining a reference-robust A. welwitschiae-associated core. The clinical Japanese–South African comparison identified 116 and 127 features, with 14 concordant KEGG orthologs involving sterol modification, protein prenylation, cofactor metabolism, redox processing, cell-wall turnover and ribosome maturation. No pathway remained significant after false discovery-rate correction; nominal pathway signals were reference-sensitive. Reciprocal projection, therefore, recovered localized cohort-associated genomic differentiation while identifying reference-conditioned effects. These findings represent differential genomic-read representation and do not independently establish copy-number variation, pathway activity, virulence or antifungal resistance.