Endophytic fungi are repeatedly presented as alternative producers of medicinal-plant natural products, yet the evidential basis of producer attribution varies from culture-based chemical detection to isotope tracing, genome analysis, transcriptional association, and functional pathway testing. This critical review examines what these different observations can and cannot establish about metabolite origin. The central problem is that the same chemical phenotype may arise through independent microbial biosynthesis, persistence of plant-derived material, microbial transformation of supplied precursors, or endophyte-mediated alteration of host metabolism. Accordingly, chemical identity and biosynthetic provenance must be evaluated separately. The reviewed evidence shows that repeated axenic cultivation and stable-isotope incorporation can provide unusually strong support for microbial production, whereas biosynthetic-gene-cluster prediction, transcript abundance, metabolomic similarity, or repeated literature citation remain incomplete forms of attribution unless connected to product formation by orthogonal tests. It also shows why culture dependence, strain variation, analytical annotation limits, and alternative host-mediated mechanisms complicate reproducibility. We propose an attribution logic in which confidence rises through convergence among authenticated biological material, independently reproducible chemical evidence, biosynthetic plausibility, and functional or tracer-based validation, while explicit competing explanations are retained until experimentally excluded. This framework is intended as a critical interpretive aid rather than a universal scoring system. Its principal limitation is the heterogeneity of available studies: many high-profile plant-like metabolites still lack pathway-complete, independently replicated evidence in their reported endophytes.
