Nowadays, there is an increase attention on the effect of selenium (Se) on metabolic processes of microorganisms. Strains belonging to the genus of Yarrowia are of great biotechnological interest for various industries. In this study, we evaluated the effect of 10 mg/L of Se on the growth and lipid production of two Yarrowia lipolytica strains: the ACA DC 50109 and one more with increased oleagenicity, derived after ALE methodology (referred here as Y. lipolytica ALE_70). The presence of Se in the growth medium negatively affected both cell mass production and total lipid accumulation, for both Y. lipolytica strains. Fractionation of total lipids showed an inhibition on neutral lipid (NL) synthesis and consequently, an increase of polar lipids (glycolipids plus sphingolipids, and phospholipids) on the lipids of the Se-enriched ACA DC 50109 strain; however, the NL/polar ratio of the Se-enriched ALE_70 indicated that Se, apart from the inhibition of NL synthesis, provoked also the accumulation of polar lipids in this strain. In addition, the fatty acid (FA) composition was differently affected by Se. Se-enriched total lipids of the ALE_70 strain were enriched in linoleic acid (C18:2 n-6), which resulted in increase of the unsaturated index. On the other hand, Se-enriched lipids of the ACA DC 50109 strain were more saturated, as the percentage of palmitic (C16:0) and stearic (C18:0) acids increased in the total FAs. Moreover, it seems that Se influenced the activity or the expression of desaturases and elongase in both strains. Finally, the supplementation of growth medium with Se affected cell morphology, as well as the size and distribution of lipid droplets inside the yeast cells. According to our opinion, Se caused stress conditions and the consequence of that was the occurrence of metabolic disorders that affected cell mass, lipid content, and/or morphological structures. The results of the present study suggest that further research should be carried out to understand the background of the lipogenesis process in yeast cells cultured under stress conditions.