Fungi and yeast species as good sources of arachidonic acid and polyunsaturated fatty acids have been attracting a lot of attention from scientists in recent years. In this study, we used the oleaginous yeast Wickerhamomyces siamensis SAKSG isolated from the gills of trout caught from the Caspian Sea. Low-cost polysaccharides hydrolyzed by enzymatic digestion of immobilized whole cells of Bacillus amyloliquefaciens ATCC 23350 served as substrates to evaluate the effects of each on the biomass and the fatty acid profiles of Mortierella alpina CBS 754.68 and Wickerhamomyces siamensis SAKSG. By using sprouted wheat, millet and wheat as starch sources adjusted to 150 g/L we obtained reducing sugar content of 102.57, 57.50 and 51.62 g/L, respectively. The highest and lowest dry weight (biomass) of M. alpina was obtained in sprouted wheat (3.7% of media) and rice-formulated media (1.72% of media), respectively. Each formulated media significantly affected the profiles of M. alpina fatty acids. The highest content of linoleic acid (41.873%), oleic acid (30.061%) and arachidonic acid (27.054%) was obtained with corn, rice and potatoes used as the carbon sources. The yeast lipid content was high, consisting of C6 up to C12 fatty acids, accounting for about 55.7% of the total fatty acids. Some amount of docosahexaenoic acid (DHA) and (ecosapentanoic acid) EPA was also observed in W. siamensis.