The dataset is a collection of marine phytoplankton production data retrieved from several sources. The main source of information consists in depth-resolved 14C primary productivity measurements complemented by chlorophyll a concentration and environmental variables. The heterogeneous data sources have been homogenized and the missing values imputed. Furthermore, we enriched the available information by adding several ancillary information related to the phytoplankton primary production. The dataset has a global spatial coverage and comprises records from 1954 to 2017. The collected data represent a valuable homogeneous and ready to use source of information for everyone interested in studying marine phytoplankton production. More information about the data and a general analysis are presented in the work: “Collection and analysis of a global marine phytoplankton primary production dataset”.