Multimedia encryption innovation is one of the primary ways of securely and privately guaranteeing the security of media transmission. There are many advantages when utilizing the attributes of chaos, for example, arbitrariness, consistency, ergodicity, and initial condition affectability, for any covert multimedia transmission. Additionally, many more benefits can be introduced with the exceptional space compliance, unique information, and processing capability of real mitochondrial deoxyribonucleic acid (mtDNA). In this article, color image encryption employs a confusion process based on a hybrid chaotic map, first to split each channel of color images into n-clusters; then to create global shuffling over the whole image; and finally, to apply intrapixel shuffling in each cluster, which results in very disordered pixels in the encrypted image. Then, it utilizes the rationale of human mitochondrial genome mtDNA to diffuse the previously confused pixel values. Hypothetical examination and trial results demonstrate that the anticipated scheme exhibits outstanding encryption, as well as successfully opposes chosen/known plain text, statistical, and differential attacks.