Simple SummaryMicroalgae are the richest source of natural carotenoids, valuable pigments, which are key components of functional food, cosmetics, drugs and animal feeding. To date, only two genera of green microalgae are widely used for mass production of carotenoids on an industrial scale, Haematococcus and Dunaliella. They produce astaxanthin and β-carotene, respectively, which are among the most useful carotenoids. In doing so one alga produces only one type of a pigment. In this paper we characterize a new strain of the green microalga Bracteacoccus aggregatus BM5/15 (IPPAS C-2045). It can simultaneously produce both carotenoids (up to 13.1 and 47.9% β-carotene and astaxanthin of cell dry mass, respectively). Growth parameters of the strain cultivated in glass bubble-column photobioreactors for commercial cultivation of microalgae were obtained. We also provide data of microscopic observations, pigment and fatty acid profile of the microalga, which are important biotechnological characteristics. Collectively, new data makes B. aggregatus BM5/15 suitable for industrial production of β-carotene, a pro-vitamin A, and astaxanthin, the most powerful antioxidant.Carotenoids astaxanthin and β-carotene are widely used natural antioxidants. They are key components of functional food, cosmetics, drugs and animal feeding. They hold leader positions on the world carotenoid market. In current work, we characterize the new strain of the green microalga Bracteacoccus aggregatus BM5/15 and propose the method of its culturing in a bubble-column photobioreactor for simultaneous production of astaxanthin and β-carotene. Culture was monitored by light microscopy and pigment kinetics. Fatty acid profile was evaluated by tandem gas-chromatography–mass spectrometry. Pigments were obtained by the classical two-stage scheme of autotrophic cultivation. At the first, vegetative, stage biomass accumulation occurred. Maximum specific growth rate and culture productivity at this stage were 100–200 mg∙L−1∙day−1, and 0.33 day−1, respectively. At the second, inductive, stage carotenoid synthesis was promoted. Maximal carotenoid fraction in the biomass was 2.2–2.4%. Based on chromatography data, astaxanthin and β-carotene constituted 48 and 13% of total carotenoid mass, respectively. Possible pathways of astaxanthin synthesis are proposed based on carotenoid composition. Collectively, a new strain B. aggregatus BM5/15 is a potential biotechnological source of two natural antioxidants, astaxanthin and β-carotene. The results give the rise for further works on optimization of B. aggregatus cultivation on an industrial scale.