Changes in plankton community structures in response to climate change and the climatic sensitivity of species are currently driving topics in marine research. In the marine environment phytoplankton consists of major primary producers, but also harmful algae that can negatively influence marine ecosystems. It is expected that climate related environmental change could result in changes in the abundance, spatial distribution, biogeography or dominance of phytoplankton species. In order to evaluate consequences of climate change for marine ecosystems it is necessary to possess high resolution information in time and space on current abundances and patterns within the phytoplankton. However, the generation of these data is constrained by a variety of reasons like the size or insufficient morphological markers of the taxa and the costs to provide samples with high spatiotemporal resolution. In the past decade the application of biosensor technology has gained significant impact in respect to microbial analysis. More and more publications describe the development of molecular sensors dedicated to the detection of microbial organisms. In the EU FP6-project ALGADEC a portable semi-automated biosensor-system has been developed in order to facilitate the detection of toxic algae in the field. This device enables the electrochemical detection of microalgae from watersamples in less than two hours, without the need of expensive equipment. This device is a prototype device that serves as a cornerstone of a new molecular based strategy for the monitoring of phytoplankton. Currently we are working on the adaptation of the biosensor to the surveillance of key species in the North Sea. And, we aim at a full automation of the system in order to provide an autonomous monitoring tool for phytoplankton. In the Future an autonomous biosensor can be combined with present in situ measurement systems for the marine environment like the FerryBox-system of the GKSS. This would serve the need for technologies that allow high resolution monitoring of marine phytoplankton in order to evaluate consequences of environmental change in the oceans. ©2009 IEEE.