Microalgae have been known as superior producers of valuable carotenoids via their defensive mechanism against environmental changes. In this study, nitrogen and phosphorus starvation (NPS), high light intensity (HL), and high salinity (HS) stress culture conditions were subjected to indigenous freshwater microalga, Mychonastes pushpae culture to investigate gene expression levels of phytoene synthase (PSY), phytoene desaturase (PDS), and zeta-carotene desaturase (ZDS) involved in carotenoid biosynthesis as well as to enhance lutein productivity. For this, the microalgal cells were cultivated in 0.5 L bubble column photobioreactors under the stress conditions. Based on the third day of culture, the lutein content of M. pushpae cultured under the NPS condition was 4.4 times higher than the control. The transcription level of PSY in M. pushpae under NPS and HL stress conditions significantly increased more than 100-fold compared to those in non-stress conditions. The expression levels of PDS and ZDS of M. pushpae increased under the culture condition with NPS, NPS & HL and NPS & HS stress compared to the control. From the results, subjecting only NPS stress to M. pushpae culture was the most effective stress for lutein production in terms of lutein productivity and carotenoid gene expression