Two genes (treY and treZ) encoding for trehalose-producing enzymes, a maltooligosyl trehalose synthase (MTSase) and a maltooligosyl trehalose trehalohydrolase (MTHase), had been cloned, expressed and sequenced from thermophilic archaebacterium Sulfolobus shibatae B12. The nucleotide sequences of treY and treZ indicated proteins with lengths of 728 and 559 amino acids and molecular masses of 86 ku and 65 ku, respectively. treY and treZ genes from S.shibatae B12 show high sequence homologies with other microbial MTSase and MTHase genes, such as S.solfataricus P2 (93% and 76% identity),S.solfataricus KM1(97% and 95% identity),Sulfolobus acidocaldarius ATCC 33909 (63% and 66% identity),Arthrobacter sp. Q36 (48% and 50% identity),Rhizobium sp. M-11(48% and 52% identity),Brevibacterium sp. (50% and 52% identity). Phylogenetic trees of these enzymes genes were constructed by analysis class of their overall nucleotide sequences. The amino acid sequences of MTSase and MTHase showed identity with members of the glycosyl hydrolase family 13 (α-amylase family). Four important regions highly conserved in the glycosyl hydrolase family 13 exist in the amino acid sequences of all these trehalose-producing enzymes. It is suggested that MTSase and MTHase are members of glycosyl hydrolase family 13 and treY and treZ maybe derived from a common original α-amylase gene.