Application of microbial lipids as an alternative source of oil was considered in the early years of 20th century. Microbial oil rich in essential polyunsaturated fatty acids (omega series) is one of the important aspects of single cell oil production. By development of technical - economical processes and also by optimization of microbial lipid production, high efficiency of microbial lipid can be provided. In this study, two standard yeast strains and four native strains were evaluated for potential of lipid production. Optimization of lipid production in these strains was carried out using design of experiments and factors affecting lipid synthesis in these strains were compared. Obtained oil was analyzed using Gas Chromatography-Mass spectrometry (GC-MS). Among the standard strains, Yarrowia lipolytica DSM8218 and the native strain Cryptococcus albidus had maximum lipid production rate of 7.65 g/L and 11.81 g/L, respectively. Application of Taguchi method was so effective in optimization of microbial lipid production and significantly increased production in evaluated strains. These lipids have potential for applications in food and pharmaceutical industries.