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Coccolithophores are well-known haptophytes that produce small calcium carbonate coccoliths, which in turn contribute to carbon sequestration in the marine environment. Despite their important ecological role, only two of eleven haptophyte plastid genomes are from coccolithophores, and those two belong to the order Isochrysidales. Here, we report the plastid genomes of two strains of <i>Ochrosphaera neapolitana</i> (Coccolithales) from Spain (CCAC 3688 B) and the USA (A15,280). The newly constructed plastid genomes are the largest in size (116,906 bp and 113,686 bp, respectively) among all the available haptophyte plastid genomes, primarily due to the increased intergenic regions. These two plastid genomes possess a conventional quadripartite structure with a long single copy and short single copy separated by two inverted ribosomal repeats. These two plastid genomes share 110 core genes, six rRNAs, and 29 tRNAs, but CCAC 3688 B has an additional CDS (<i>ycf55</i>) and one tRNA (<i>trnL-UAG</i>). Two large insertions at the intergenic regions (2 kb insertion between <i>ycf35</i> and <i>ycf45</i>; 0.5 kb insertion in the middle of <i>trnM</i> and <i>trnY</i>) were detected in the strain CCAC 3688 B. We found the genes of light-independent protochlorophyllide oxidoreductase (<i>chlB</i>, <i>chlN</i>, and <i>chlL</i>), which convert protochlorophyllide to chlorophyllide during chlorophyll biosynthesis, in the plastid genomes of <i>O. neapolitana</i> as well as in other benthic Isochrysidales and Coccolithales species, putatively suggesting an evolutionary adaptation to benthic habitats.