Toxicological, biological and molecular effects of two eco-friendly botanical oils named Jojoba andJatropha oils against the newly molted 2^nd instar larvae of the Egyptian cotton leafworm, Spodoptera littoralis (Boisd.), were investigated under laboratory conditions. Results generally revealed a decrease in the mean larval, pupal, and adult durations for the 2^nd instar larvae surviving treatment with the LC₅₀ value 1.905 % and 1.793 %, for the two tested oils Jojoba oil andJatropha respectively. Also, plant extracts caused a reduction in all the other biological impacts (pupation, adult emergence percentage, the mean number of eggs/female and the mean number of hatched eggs). Molecular studies have been carried out on 6^th instar larvae of S. littoralis which treated in 2^nd larval instars with LC₅₀ of the tested botanical oils. Seven random primers were used in this study to generate a fragmenting pattern as a tool to investigate the molecular differences between treated samples and control. The numbers of unique and common fragments generated by using these primers (O4, O7, O5, O14, C10, C13 and C15) were recorded. It has been found that primer C13 was the most powerful one in generating a unique informative fragmenting pattern; it gives five specific unique fragments. While the primer O14 was the poorest one in generating an informative fragmenting pattern.