Data collected within the EMBLAS-II "EU-UNDP Project 'Improving Environmental Monitoring in the Black Sea' (EMBLAS-II)" (http://emblasproject.org/). EMBLAS-II is co-financed by the European Commission (EC) and United Nations Development Programme (UNDP). The project implementation started on 1 April 2014 and ended on 31 May 2018, having the total duration of 50 months. The EMBLAS project is addressing the overall need for support in protection and restoring the environmental quality and sustainability of the Black Sea. The specific objectives are as follows: Improve availability and quality of Black Sea environmental data in line with the MSFD and Black Sea Strategic Action Plan (2009) needs; Improve partner countries' ability to perform marine environmental monitoring along MSFD principles, taking into account the Black Sea Diagnostic Report II recommendations on capacity building. The National Pilot Monitoring Studies (NPMS) and Joint Open Sea Survey (JOSS) Programme was developed within the framework of Project Activities. The NPMS-2017 (Phyllophora) was performed in period 2017.04.11 to 2017.04.13 in the Ukrainian waters (North-Western part of the Black Sea) in the area of the MPA Zernov’s Phyllophora Field onboard the M/V "Auguste Piccard" (Ukraine). Microzooplankton samples were taken within Zernov Phyllophora Field. In total, 16 samples were taken in April (surface, picnocline and bottom layers). Bouin’s fixed water samples (sample volume was 930 - 985 cm3) were concentrated by settling up to volume 5 cm3 after delivery to the laboratory. Sampling performed by O. Kurilov (IMB NANU).