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Sulfitobacter pseudonitzschiae H46, a marine bacterium associated with microalgae, exhibits algicidal activity against harmful algal bloom microalgae Chattonella marina and Alexandrium tamarense. The complete genome of S. pseudonitzschiae H46 was sequenced to investigate its algicidal mechanism further. One chromosome, eight circular plasmids and add one not circularized plasmid (Plas II) were identified, which are 4.93 Mb in length with 4871 open reading frames. The genome contains 43 transfer RNA (tRNA) genes; six ribosome RNA (rRNA) genes that can be classified into two 5S rRNA, two 16S rRNA, two 23S rRNA, and two small RNA (sRNA) genes. Genomic annotation revealed that S. pseudonitzschiae H46 has two pairs of LuxI/R-type Quorum-sensing (QS) systems. The QS systems can regulate the functions involved in host colonization and biofilm formation. Moreover, the existence of 49 Type-IV and Dddl genes in the chromosome indicated that Dimethylsulfoniopropionate (DMSP) catabolism of S. pseudonitzschiae H46 is the main interaction with marine microalgae. S. pseudonitzschiae H46 utilizes DMSP produced by microalgae as the carbon source, and this may induce algicidal activity. The complete genome sequence of S. pseudonitzschiae H46 can provide useful information on the underlying molecular mechanism between QS and algicidal activity., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)