Adenine phosphoribosyltransferase (APRTase) is an important enzyme for its ability to convert adenine, a byproduct of many biochemical reactions, into AMP. By functional complementation of an Escherichia coli mutant, cDNAs encoding two APRTases have been cloned from Arabidopsis thaliana. One of the cDNAs (ATapt1) has been previously identified while the second (ATapt2) is of a previously unknown type. Kinetic analysis of the two enzymes purified from E. coli expressing the two cDNAs indicates that ATapt2 has a higher affinity for cytokinin than the ATapt1. RNase protection studies indicate that the ATapt2, is not expressed in leaves. Analysis of the gene structure indicates that ATapt2 has identical intron positions to ATapt1, but neither the intron sequence nor intron size are conserved between the two genes. The implications of a second, differentially expressed APRTase with affinity for both adenine and cytokinin are discussed.