Eighty-nine cultured Pseudomonas species isolated from the sediment and water samples collected from five industrial Red Sea regions that have been affected by petroleum and industry. Genotypic (exoT, exoS, exoU, exoY, lasA, lasB, rhlA, rhlB, Pf1, PAGI-1, -2, and -3) and phenotypic (DNase, elastase, lipase, protease, siderophore, antibiotic resistance patterns) characteristics were determined. Out of these isolates, nine Pseudomonas isolates were selected as the hyperactive virulence factors producers along with highly resistant pattern against all antibiotics of different classes included in this study. They were subjected to phenotypic and chemotypic characterization as well as molecular identification through 16S rRNA gene amplification and sequencing. The bioactive metabolites of these nine strains were extracted by ethyl acetate followed by evaluating their cytotoxic activity toward liver tissues, kidney tissues, and other biochemical activities in rat. Both EGY6 and EGY8 caused the highest significant reduction in the levels of packed cell volume (PCV), red blood cell count (RBC), and hemoglobin (Hb), which indicate that these Pseudomonas strain metabolites could cause anemia and toxic effects on hematological values in animals that were infected with them. Rats treated with the most toxic extract, EGY8, showed severe histopathological alterations in liver and kidney.