Endometriosis and polycystic ovary syndrome (PCOS) are two common gynecological disorders that may co-occur in a subset of infertile women, yet their pathophysiological overlap has been historically underestimated. This review synthesizes recent evidence on biomarkers of ovarian dysfunction in infertile women with these conditions, focusing on clinical, cellular, and molecular studies. We identify five major biomarker categories: inflammatory markers (IL-6, TNF-α, PTX3, Tenascin-C, HMG-1), oxidative stress markers (Fe² ⁺ , MDA, AGEs, SESN2), hormonal regulators (AMH, Activin A, Follistatin, Vasorin, MG53), metabolomic and proteomic profiles, and epigenetic regulators (exosomal miRNAs including miR-22-3p, miR-145-5p, miR-320a, and HDAC9, YAF2, CDC6). Most of these biomarkers remain at the exploratory or single-cohort stage, and none has yet been externally validated or incorporated into clinical guidelines. Key findings include the observation that AMH interpretation in women with both conditions remains challenging, because the independent effects of PCOS and endometriosis on ovarian reserve may coexist and potentially offset each other, although direct evidence on their interaction is currently lacking; the candidate diagnostic potential of non-invasive biomarkers such as Vasorin for PCOS and SESN2 for endometriosis, both of which derive from single studies without external validation; and the convergence of chronic low-grade inflammation and oxidative stress as shared pathogenic pathways. The evidence base is heterogeneous and predominantly exploratory. These candidate biomarkers may in the future support early detection, risk stratification, and personalized therapeutic strategies in assisted reproductive technology, but only after analytical and clinical validation in independent, prospective, multi-ethnic cohorts; if validated, they could contribute to reducing diagnostic delays and improving reproductive outcomes.