Virus diseases, especially those caused by mixed infections, are among the economically most devastating diseases of sweet potato. Sweet potato virus disease (SPVD), which is caused by mixed infection of Sweet potato feathery mottle (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV), is the most widespread in East Africa. Lack of rapid and sensitive techniques for detecting the two viruses makes their control almost impossible. In this study, a multiplex polymerase chain reaction (mPCR) protocol was developed and subsequently evaluated for its effectiveness in simultaneous detection of SPFMV and SPCSV using 13 samples. Total RNA extracts were subjected to reverse transcription followed by PCR with two sets of virus-specific primers. DNA bands of 703 and 235 bp were obtained for SPFMV and SPCSV, respectively. No amplification products were obtained from healthy controls. Results obtained from nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA) confirmed the efficiency of the mPCR protocol. We recommend the developed mPCR technique for routine molecular diagnostic purposes.