Fucoxanthin has been reported as bioactive compounds exhibiting strong antioxidant, anticancer and anti-inflammatory activities. Owing to its a wide range of applications and potentials, commercial production of fucoxanthin from algae has been attracted many attentions. Although, most of seaweeds and diatoms contain fucoxanthin as major carotenoid contents, low productivity of fucoxanthin still hinder the industrial application. Here, we newly isolated and identified indigenous marine diatom Odontella sp. BS-003 as a resource of fucoxanthin production. The characterization, optimization and production of the fucoxanthin, along with other bioactive compound omega-3 fatty acid from odontella sp. BS-003 were analyzed in this study, and the results represented optimal culture condition (two-fold silicate containing F/2 medium) significantly enhanced the algal biomass productivity. The maximum biomass (1.83 g/L), fucoxanthin (3.88 ㎎/g), along with omega-3 fatty acid (10 %, w/w) were obtained from the 10 L of photobioreactor. Based on the results, it is speculated that the microalga Odontella sp. BS-003 can be a promising natural resource for the production of bioactive compounds.