Phytophthora blight is a devastating disease of pigeon pea (Cajanus cajan) that severely impacts plant growth and productivity. This study investigates the morphological, anatomical, and biochemical responses of a susceptible variety (ICPL 11260) and a resistant variety (IPAC-02) following infection by Phytophthora. Morphological analyses showed that infection caused a drastic reduction in root length, shoot length, leaf number, fresh weight, and dry weight in the susceptible ICPL 11260 variety, with reductions ranging from 0.5- to 2-fold compared to non-infected controls. Anatomical observations revealed pronounced cellular damage and mycelial invasion in infected ICPL 11260 plants by 30 days after infection, whereas infected IPAC-02 plants exhibited no fungal colonization. Biochemical analyses further demonstrated that the resistant IPAC-02 variety accumulated higher levels of total soluble sugars, proteins, phenols, and flavonoids, along with increased activities of defense-related enzymes (chitinase and β-1,3-glucanase), compared with the susceptible ICPL 11260. Under P. cajani stress, IPAC-02 maintained significantly elevated osmolyte concentrations (total sugars 153.7 mg g⁻¹ FW; proteins 25.4 mg g⁻¹ FW), secondary metabolites (phenols 51.7 mg g⁻¹ FW; flavonoids 33.1 mg g⁻¹ FW), and PR-enzyme activities (chitinase 11.4 U mg⁻¹ protein; β-1,3-glucanase 9.1 U mg⁻¹ protein). These responses support a lignification-mediated defense mechanism in IPAC-02 and highlight its potential value for breeding Phytophthora-resistant pigeon pea cultivars.