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Partitions of the cytochrome oxidase subunit 1 (CO1) gene, especially the 5′ end, are frequently recruited to infer lower level phylogenies in animals. In diploblasts, mitochondrial genes were found to evolve in a slower rate than their bilaterian counterparts. Therefore, diploblast CO1 gene trees repeatedly remained unresolved, which also raises doubts on the suitability of CO1 for DNA barcoding in these animals. The complete mitochondrial genome sequences from Anthozoa and recently from Porifera allow us to compare the resolution power of the 5′ partition, which has also been proposed as the standard marker for DNA barcoding, with a less frequently used partition further downstream. We report on the finding of significantly different substitution patterns of the downstream partition opposed to the 5′ partition. We discuss the consequences and potential in the light of diploblast phylogenetic reconstruction …