Background: Melanin (Mel) is a naturally occurring pigment made by some microorganisms. Streptomyces sp and Aspergillus niger are capable of producing a high quantity of brown (Mel1) - black (Mel2) intercellular Mel pigments. Aim: To compare between melanin-producing Streptomyces sp and Aspergillus niger productive efficiency and tolerance against lead and cadmium ions stress was investigated. Materials and Methods: The tested strains were identified by molecular characterizations (16S rRNA & 18S rRNA) gene sequence, Mel1 of S. longisporoflavus NR043926 and Mel2 of A. niger MT355517 were extracted and purified from the dried microbial biomass. Physicochemical characterizations of extracted Mel pigments were compared with standard melanin based on infrared (IR) analysis. The productive efficiency and tolerance under absorption capacity of the selected strains against lead and cadmium ions were identified as  the minimum inhibitory concentration (MICs) of each metal ions. Results: The production of Mel pigments and growth of two selected strains were decreased gradually by increasing the concentration of cadmium or lead from (10-750 ppm). Transmission electron microscopic examination showed heavy metals binding occurred on the surface of the microorganism cells, uptake or precipitation inside the melanized inner cell wall, finally vacuoles and microbial cells damage. Conclusion: A. niger can resist cadmium and lead ions more than S. longisporoflavus, Mel2 had a high protective function toward the stress of the heavy metal in comparison to Mel1.