CardioPhylo uses phylogenetic footprinting method to predict conserved transcriptional factor binding sites (TFBSs) in cardiac genes involved in heart development and congenital heart defects. The program obtains the annotated Position Weight Matrix (PWMs) corresponding to cardiac transcription factors (TFs) from CardioSignal database and visualizes the identified TFBSs within cis-regulatory region. We hope this program could help researchers to evaluate their experiment results and facilitate their understanding of cis-regulation in heart system.