Abstarct: Microorganisms that have a lipid accumulation capability more than 20% of their biomass are called oleaginous. Mortierella alpine fungi species are famous oleaginous fungi. The most important product of Mortierella alpine is lipid with high content of the arachidonic acid fatty acids. In this research the effect of pHysic chemical factors and magnesium nano-particles on the oil production from Mortierella alpina fungus in a submerge fermentation condition as well as theirs relation with the rate Malic gene exxpression and housekeeping genes were investigated. The results showed that at the early fermentation time until third days, a considerably biomass growth was observed. during the 24 after that time, the growth trend had slowed down, subsequently at the end of fermentation time, a deterioration in biomass accumulation was occurred. More to the point, the consumption of the reducing glucose was coincident with the accumulation of biomass. at the days two and five in a non-nano particle medium, translation elongation factor 1 alpHa as housekeeping gene had the maximum gene exxpression among the selected genes at the 3 and 5 days of fermentation time. To select a suitable housekeeping gene, the gene that has the lowest variation in exxpression at the stage of growth and death must be investigated. The dihydropteridine reductase at this stage was confirmed as the best candidate gene with the most stability index. Nano-particles in media induced the growth rate comparing to the control sample. Dihydropteridine reductase and putative 60S ribosomal with a suitable best keeper index and low Standard deviation, CV index and factor M1 were chosen in the fermented medium containing nano-particles. However, in both cases, the dihydropteridine reductase gene was selected as the best housekeeping gene for further processing; hence the gene was used to normalize the malic enzyme gene exxpression. The results of the fold-change of the malic enzyme in a nano-sample to the non-nano-sample indicated that, nano-particle had positive effect on the malic gene exxpression and the highest effect was achieved at the begging of the fermentation time that caused the lipid production to induce.