<jats:title>ABSTRACT</jats:title> <jats:p> Members of the bacterial phylum <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence <jats:italic>in situ</jats:italic> hybridization (CARD-FISH). Generally <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> abundance was correlated to the <jats:named-content content-type="genus-species">Centrales</jats:named-content> diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ∼90% of the <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> reside in the &gt;3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named <jats:named-content content-type="genus-species">Planctomyces</jats:named-content> -related group A, uncultured <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> group B, and <jats:named-content content-type="genus-species">Pirellula</jats:named-content> -related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> group B was most abundant in autumn samples, while <jats:named-content content-type="genus-species">Planctomyces</jats:named-content> -related group A was present in high numbers only during late autumn and winter. The levels of <jats:named-content content-type="genus-species">Pirellula</jats:named-content> -related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the <jats:named-content content-type="genus-species">Planctomycetes</jats:named-content> is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates. </jats:p>