<p>The dataset contains phytoplankton data collected in the Black Sea between 2001 and 2005 and processed by Andrei C., Anghel A., Boicenco L., Ionescu C., and Sburlea A. The data were collected from shallow to shelf Romanian waters from various transects such as Sulina, Mila 9, Portita, and Sf. Gheorghe (northern zone, strongly influenced by the freshwater input from the Danube Delta) to Constanta, Mangalia, and Vama Veche (southern zone). The sampling was carried out from standard depths with Niskin bottles. From each depth was collected a sample of 500 ml. The standard sedimentation technique for sample preparation was used (Morozova-Vodianitkaia, 1954). The scientific team identified and counted the phytoplankton species from a subsample with an inverted microscope and calculated the total abundance and biomass of each species. This dataset was compiled from a collection of phytoplankton datasheets and contains abundance (cells per liter) and biomass (mg/m3) data for individual phytoplankton taxa.</p>