The biosynthesis of trehalose is catalyzed by synthase enzyme complex and degraded by neutral trehalase enzyme. Yarrowia lipolytica is a dimorphic yeast and used as a model organism for understanding the lipid metabolism of higher eukaryotes. YlTPS1 and YlNTH1 genes are responsible from the recycling of trehalose in Y. lipolytica. The aim of this work is to determine the expression patterns of YlTPS1 and YlNTH1 genes under different carbon sources by using RNAseq study. The files used in this analysis were obtained from the EMBL-EBI data bank and Study ID is “PRJEB2863”. The substrates used in the work are Alkane, Glucose, Glycerol, Oleic Acid, Tributyrin and Triolein. The run accession numbers of substrates are ERR073010, ERR073011, ERR073009, ERR073008, ERR073012 and ERR073007, respectively. "Trimmomatic" tool was used for croping the readings in the next generation sequencing files. Reference genome of Y. lipolytica were obtained from Ensembl genome data base. The files were converted to “ERR0730xx_tophat2.bam” files and used in the "FeatureCounts" tool. We found that the transcript level of YlTPS1 gene was 2 to 4 times higher than YlNTH1 gene. The rate of trehalose synthesis is greater than the rate of breakdown in Y. lipolytica yeast cells.