Effects of the lethal concentrations of Chlorfluazuron and Bacillus thuringiensis (Diple D.f.) against Pectinophora gossypiella (Saund.) larvae treated as neonate were studied recently. The obtained results indicated that, Chlorfluazuron treatment showed great toxicity compared to B. thuringiensis. The biochemical response of 10-days old larvae was studied by the evaluation of the total soluble protein, total lipids, and transaminases activities: Alanine aminotransferase (ALT) and Aspartate aminotransferase (AST), and the carbohydrate hydrolyzing enzymes (trehalas, invertase and amylase). The total protein content decreased to 43.26mg/dl and 26.24mg/dl for chlorfluazuron and Bacillus thuringiensis treatments, respectively compared to untreated control (100.1 mg/dl). In contrast, the total lipid levels were increased for the same compounds, recording values: 132.73 and 87.87 mg/dl, respectively, compared to control (36.51 mg/dl). Moreover, a high increase in the activity of all Carbohydrate hydrolyzing enzymes induced by both treatments compared to control. Activity of AST enzyme was declined to 5.44 and 12.66 mg glucose released/gm body weight/min for Chlorfluazuron and B. thuringiensis, respectively, compared to control (14.62 mg glucose released/gm body weight/min). In contrary, a great increase in the ALT activity was recorded with values: 129.49 and 159.61 mg/dl for the same compounds, respectively compared to untreated check (85.36 mg/dl). Newly hatched larvae of P. gossypiella treated with Chlorfluazuron as one of chitin biosynthesis inhibitors showed some histopathological alternations of the cuticle layers. The exo-cuticle became thicker with variable staining affinity, while the endo-cuticle became thin and faintly stains. The epidermal layer was formed mostly with irregularly distributed cubical cells varied in height and staining affinity. Furthermore, histopathological alternations, of midgut were obtained for Bt treated larvae of P. gossypiella representing extensive damage of the epithelial columnar cells with increased cytoplasm vacuolation at the Bt toxins. In addition, ultrastructure studies conjugated with observations for both Chlorfluazuron and Bt treated and untreated PBW larvae were massive supported by transmission electron microscopy (TEM).