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Finnish Institute of Marine Research (FIMR) as a founding member of Alg@line consortium has been a forerunner in the field of monitoring research using commercial ferries. In 1992 FIMR started continuous measurements on board the ferry Finnjet, crossing the Baltic Sea Proper, using unattended recording and sampling system. During the spring of 2007 the ferrybox monitoring system was reinstalled in a new ferry Finnmaid providing real time observed data transmission with satellite connection. Chlorophyll-a (Chla) still remains the principal monitoring parameter. However, the distribution of cyanobacteria cannot be evaluated using Chla in vivo fluorescence, as most of their Chla is located in the poorly-fluorescing photosystem I. Instead, phycocyanin (PC) fluorescence is used in the detection of cyanobacterial blooms in 2005-07. PC fluorescence shows a linear relation to the biomass of the bloom forming filamentous cyanobacteria. During blooms of filamentous cyanobacteria the variability in Chla concentrations is better explained by PC fluorescence than by Chla fluorescence. Additionally, Chla records have been applied in validation of MODIS satellite monitoring for the water quality.