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¹ İskenderun Teknik Üniversitesi – Deniz Bilimleri ve Teknolojisi Fakültesi, Meydan Mah. 512, 31320, İskenderun / Hatay DOI : 10.17693/yunusae.vi.286302 Viewed : 3053 - Downloaded : 2279 In this study, High Performance Liquid Chromatographic (HPLC) and Spectrofluorometric methods commonly used in determining of phytoplankton groups were compared. For this purpose, totally 152 water samples were collected in four different periods (July-September 2012 and March-May 2013) from five stations representing different ecosystems between Mersin Bay and Rhodes Island filtered by using different types of filters. Chlorophyll a, picoplankton, nanoplankton and microplankton parameters were compared by using HPLC and spectrofluorometric methods. The HPLC was found to be more sensitive than the spectrofluorometer, but it was determined that the GF/F filters used in the method failed to retain the picoplanktonic cells. GF/F filters used in seas where the concentration of picoplankton is high, such as the Mediterranean, may cause biomass loss as compared to nucleopore polycarbonate filters, causing false readings. Chlorophyll-a and microplankton measurements were found to be compatible with each other when using both methods. Keywords : Cholorophyll-a,Pigments,Picoplankton,Nanoplankton,Microplankton