The present study was conducted to isolate, identify, and extract the lutein from a biflagellate Proteomonas sulcata from the coastal waters of the Gulf of Mannar, Southern east coast of India. The targeted unicellular biflagellate P. sulcata belonging to the group Geminigeraceae was collected and isolated using 96 well plates followed by the serial dilution method and morphologically confirmed. However, the pure isolate was also confirmed based on molecular identification by PCR and sequence analysis of 18 S rRNA. The resultant sequence was analysed and reflected in phylogenetic tree. Optimised the environmental parameters to obtain the maximum cell density of 50.36 ± 0.81 × 105 cells/ml. The unique characteristic feature of the isolate was the change in colour during the culture phases. ie., red colour in growing phase up to 6th day in haffkine flask and changed into green during the stationary phase until the death phase. The reason for the colour change might be due to phycobiliprotein present in the microalga and also confirmed by FTIR analysis. The maximum chlorophyll content and carotenoid of 4.59 ± 0.38 mg/g 2.55 ± 0.12 mg/g was estimated. The conventional lutein extraction process such as saponification and solvent extraction methods was followed. The process was optimized and extracted crude lutein was analysed by using HPLC. The present study concluded that, the maximum lutein yield of 3.96 ± 0.1 mg/g was obtained at a 6 M concentration of KOH and also found that the highest amount of lutein was obtained from wet biomass (red-coloured biomass) of 4.72 ± 0.38 mg/g which is significantly higher than that of freeze-dried biomass.