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The genus <i>Cocconeiopsis</i> was separated from <i>Navicula</i>, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with <i>Cocconeiopsis kantsiensis</i> and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of <i>C. kantsiensis</i> was most similar to those of three <i>Navicula</i> species and <i>Halamphora americana</i>, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for <i>Phaeodactylum tricornutum</i>. The multigene phylogeny reconstruction showed that <i>Cocconeiopsis</i> was sister to <i>Didymosphenia</i> but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed <i>Cocconeiopsis</i> was sister to <i>Cocconeis</i>, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and <i>Cocconeiopsis</i> diverged with monoraphid <i>Cocconeis</i> about 58.9 Ma. Our results support the assignment of <i>Cocconeiopsis</i> to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of <i>Cocconeiopsis</i>.