The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.