Protozoa are unicellular, mutualistic or parasitic responsible for several diseases of humans, animals and plants. Role of protozoa ATP-binding cassette (ABC) transporters is known as membrane proteins mediate the ATP-dependent transport of a wide variety of chemotherapeutic drugs away from their targets inside the parasites. The gene sequences of many protozoans have recently been available. The protozoan phylogeny has been always challenging relating to their evolutionary relationships. In the current study an attempt has been made to study the phylogenetic relationships among selected protozoan species based on ATP-binding cassette transporter gene along with their corresponding RNA secondary structures.