Circadian oscillations are ubiquitous among organisms and rely on a positive element being repressed by a negative element to complete a transcription-translation feedback loop (TTFL). The complexity of this loop and secondary loops have evolved over the animal linage. The circadian clock mechanism is well described in many deuterostome and higher protostome species, particularly in insects. Less is known in lower animals; however, the circadian clock mechanism has been at least partially elucidated in a few key species of sponges, cnidarians, annelids and crustaceans. Here, we identified the negative regulators PERIOD and CRYPTOCHROME of the Acoelomorphan, Isodiametra pulchra . The Acoelomorpha are an especially important group to study because are the common ancestor of the protostome-deuterostome bifurcation, retaining characteristics of both deuterostomes and protostomes that have made an agreement on their positioning difficult. We previously reported the discovery of a primitive PER In this species, pin-pointing the origin of PER in the Animalia. Here, we report the identification of a CRY ortholog using bioinformatic approaches. We also used predictive modeling to test if I. pulchra PER and CRY can form a heterodimer. Using HADDOCK predictive modeling we found a conserved loop containing TRP253 on the I. pulchra PER homologue that fits into a binding pocket on I. pulchra CRY homologue. Ongoing research from our lab is using E. coli to express these proteins for a Surface Plasmon Resonance assay to determine if these proteins bind to validate the in silico HADDOCK results.