Ochrophyte microalgae attract attention from the applied phycology perspective, due to their ability to grow rapidly, engage variable trophic modes, and simultaneously produce high-value compounds such as xanthophyll carotenoids and polyunsaturated fatty acids. Unlike more often considered marine diatoms and haptophytes, unicellular chrysophytes may represent a reasonable freshwater alternative. In this work, we introduced two representatives: Chlorochromonas danica (Ochromonadales) and Hibberdia magna (Hibberdiales). We compared their ability to produce target compounds in mixotrophic and photoautotrophic modes, respectively. Both organisms had a similar temperature optima (18–22 °C), but light demands were much higher in the photoautotrophic H. magna. This work is the first report of fucoxanthin content and productivity by C. danica, showing that the presence of light enhanced the content of fucoxanthin 4.5-fold compared with darkness. For fucoxanthin productivity in the mixotrophic batch cultured C. danica, the optimal initial glucose dose was 10 g L−1. Culture medium supplemented with mineral nutrients resulted in an increase in biomass and fucoxanthin productivity of C. danica achieving the highest biomass productivity of 0.81 ± 0.06 g L−1 d−1. H. magna accumulated a maximum of 4.54 ± 0.04 mg g−1 DW of fucoxanthin, which was slightly more than the maximum value for C. danica of 3.99 ± 0.19 mg g−1 DW. However, due to the lower biomass productivity of H. magna, the maximal fucoxanthin productivities reached very similar values of 1.15 ± 0.05 and 1.16 ± 0.01 mg L d−1 in C. danica and H. magna, respectively. Both organisms had a relatively high fatty acid content, accounting for 17 % and 19 % of DW in C. danica and H. magna, respectively. H. magna had a higher level of polyunsaturated fatty acids, which were more diverse, longer, and more unsaturated. The potential for utilization of selected chrysophytes as producers in a multi-target biorefinery is discussed.