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Plankton monitoring by microscopy offers a long-term ecological perspective of plankton communities, but detection approaches are uniquely biased. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assesses the value that genetic methods bring to microscopic and flow cytometry monitoring methods in the Western (English) Channel. An 18S high throughput sequencing (HTS) diversity survey of plankton taxa was performed on samples collected from an automated Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR) from 2011–2012. This survey detected contrasting but complementary taxa assemblages to that of microscopic surveys, mostly composed of smaller or naked or thin-walled plankton taxa, with most phytoplankton being under 10 µm infrequently recorded by other surveys. Most genetically-detected taxa in the survey were mixotrophic or heterotrophic. In comparison with microscopic phytoplankton counts from the CPR survey and Western Channel Observatory station L4, only 8–12 taxonomic families were common to all three surveys, most of them dinoflagellates, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. Additional quantitative real-time PCR detection of two potentially harmful taxa, the pelagophyte, Aureococcus anophagefferens and four Pseudo-nitzschia from 2011–2013. This revealed that growth of A. anophagefferens was elevated in the summer of 2011, whilst the appearance of Pseudo-nitzschia delicatissima in February of that year contrasted with it's timing at a coastal station. Smaller phytoplankton measured by flow cytometry had distinct seasonality and abundance in the mid-Atlantic compared to coastal regions reflecting distinct conditions. [ABSTRACT FROM AUTHOR]