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Hybridization between genetically distinguishable taxa provides opportunities for investigating speciation. While hybridization is a common phenomenon in various macro-organisms, natural hybridization among micro-eukaryotes is barely studied. Here we used a nuclear and a chloroplast molecular marker and morphology to demonstrate the presence of natural hybrids between two genetically and morphologically distinct varieties of the marine planktonic diatom Pseudo-nitzschia pungens (vars. pungens and cingulata) in a contact zone in the northeast Pacific. Cloning and sequencing of the rDNA internal transcribed spacer region revealed strains containing ribotypes from both varieties, indicating hybridization. Both varieties were found to also have different chloroplast-encoded rbcL sequences. Hybrid strains were either hetero- or homoplastidial, as demonstrated by denaturing gradient gel electrophoresis, which is in accordance with expectations based on the mode of chloroplast inheritance in Pseudo-nitzschia. While most hybrids are probably first generation, there are also indications for further hybridization. Morphologically, the hybrids resembled var. pungens for most characters rather than having an intermediate morphology. Further research should focus on the hybridization frequency, by assessing the spatial and temporal extent of the contact zone, and hybrid fitness, to determine the amount of gene flow between the two varieties and its evolutionary consequences.