The dataset compiles in situ observational data obtained during the R/V Mirai MR16-09 cruise (2017-01-21 to 2017-02-03) off western Patagonia, Chile. The biological data provides information of primary production, total chlorophyll-a, as well as, phytoplankton species composition (abundance of diatoms and dinoflagellates). Water samples for total Chlorophyll-a and phytoplankton cell abundance were collected at the same sampling depths as nutrients. The total Chlorophyll-a was measured by filtering 280 mL of seawater at low vacuum pressure (<0.02 MPa) onto 25 mm Whatman GF/F filters. After filtration, phytoplankton pigments were immediately extracted in 7 mL of N,N-dimethylformamide and stored at -20°C until fluorometric analysis (Turner Design 10-AU-005). Quantification and taxonomical classification of the main dinoflagellates and diatoms taxa, were done using sub-samples in a 25 mL sedimentation chambers using an inverted microscope (CXK-41 Olympus). Diatoms and dinoflagellates were identified at species or genus level. Primary production rate was calculated using the equation proposed by Hama et al. (1983).