Background and Objective: Production of pigments by microorganisms has significant importance than other sources; because microorganisms are grow quickly, easier extraction and higher yields. The purpose of this study was isolation and identification of pigment-producing microorganisms from soils in regions of West Mazandaran province in the second half of 1389 and toxicity effect pigments.Materials & Methods: 70 soil samples from the Mountain West Mazandaran province (Chalus, Tonekabon and Ramsar) were collected and after of prepared serial dilution, each of samples was cultured on Nutrient agar and Sabouraud Dextrose Agar. After, colonies were selected with the ability to produce pigment. Pigment extraction was done by Methanol extraction on Sediment microorganisms. Different color compounds were identified by TLC. Molecular identification of microorganisms was performed by rDNA PCR Sequencing. Also, oral acute toxicity of pigments were evaluated on the albino mice.Results: Seven microorganisms were identified include Aspergillus sp, viridians Aerococcus, Methyl bacterium sp, Bacillus sp, Eurotium rubrum, Micro bacterium testacies and Acinetobacter johnsonii. Oral acute toxicity study of the Pigments on rats was no mortality in the maximum dose. However, studies of liver enzymes and liver histopathology were showed the pigments reversible toxic effect on the liver tissue in maximum dose.Conclusion: As regards the natural pigments in the proper doses are healthier than their chemical, their application is useful in different industries. Also to determine the structure of this pigment and to removal of toxic groups of pigments can be used in various industries.