Marker pigments are used as a proxy for biomass of distinct phytoplankton classes in 15 different oceanic regions. However, sometimes disagreements are observed between microscopy and 16 accessory-pigment based approaches in distinct regions mainly due to changing environmental factors 17 governing diversity and structure of community composition. In this study, concordance between 18 microscopy and HPLC-CHEMTAX methods were investigated first time in coastal waters of Erdemli, 19 Turkey, in the Levantin Basin of the northeastern Mediterranean Sea by weekly intervals during 2015-20 2016. According to our results, marker pigment of diatoms, fucoxanthin, which was the most 21 prominent pigment in the study area during most of the year, was a better indicator of diatom 22 abundance than diatom carbon biomass. CHEMTAX derived values of diatom chlorophyll a (Chl a) 23 were not in concert with either abundance or carbon biomass of this group. Contribution of 24 dinoflagellates and cryptophytes to the phytoplankton community was underestimated with pigment 25 based approach. Accessory pigment of cyanophytes, zeaxanthin, was also an important pigment in the 26 samples. Biomass of haptophytes seemed to be overestimated by HPLC-CHEMTAX analysis. In 27 contrast to diatoms, CHEMTAX derived chlorophyll a values of cryptophytes were correlated with 28 abundance of this group but not with alloxanthin. Inclusion of live counts of nanoplanktic 29 cryptophytes, haptophytes and prasinophytes provided a better correlation between microscopy and 30 pigment based results. According to CHEMTAX analysis, nanoplankton and picoplankton constituted 31~55% of Chl a in the region.32 33 Mediterranean Sea 4 [1, 2, 3]. Among these parameters phytoplankton cell counting and calculation of cell volume is a 5 process of extremely fatiguing and time consuming and not very suitable for analysis of high number 6 of samples. For estimating standing stock from Chl a values obtained either through satellites or direct 7 seawater measurements in a region, factors influencing C:Chl a ratios should be considered. This ratio 8 varies between <10 and >200 among different phytoplankton classes as well as with change in nutrient 9concentrations, temperature, irradiance, growth phases and from species to species [3, 4, 5, 6, 7, 8]. 10 Each of these parameters are variable in different seawater regions and should be validated with field 11 data in less-studied locations. Chl a content of each phytoplankton group can be estimated based on 12 their marker pigments determined by HPLC-CHEMTAX analysis and from these groups specific Chl 13 a values, carbon biomass of phytoplankton groups could be assessed. HPLC analysis is faster than 14 microscopy and provides one step analysis of all size groups through retention of pico-nano-and 15 micro-phytoplankton on filters [9, 10]. However, verification of results obtained from pigment based 16 approach by microscopy is a necessity at least for some of the samples due to sharing of some marker 17 pigments by different phytop...