Trichoplax genome contains about 98 million base pairs and 11,514 predicted protein-coding genes.

All nuclei of placozoan cells contain six pairs of chromosomes that are only about two to three micrometres in size. Three pairs are metacentric, meaning that the centromere, the attachment point for the spindle fibers in cell division, is located at the center, or acrocentric, with the centromere at an extreme end of each chromosome.