Molecular cloning of the gene of hexaprenyl diphosphate synthase (HexPS) of Micrococcus luteus B-P 26 was achieved, and the gene of heptaprenyl diphosphate synthase (HepPS) of Bacillus subtilis was also identified. We have already reported the cloning of the gene of HepPS of Bacillus stearothermophilus and revealed that the two essential components of this enzyme (Component I' and Component II') were encoded by the first and the third out of the three neighboring open reading frames. DNA sequence analyses of the genes encoding HexPS of M. luteus B-P 26 and HepPS of B. subtilis revealed that the locations of these genes were very analogous to that of HepPS of B. stearothermophilus. The first and the third genes of them were found to encode the two components of medium-chain prenyl diphosphate synthases (Component A and Component B of HexPS or Component I and Component II of HepPS), respectively. The deduced amino acid sequences of the larger subunits (Component B, -II and -II') have the seven highly conserved regions typical of prenyltransferases. The smaller subunits (Component A, -I and -I') have no similarities to any proteins currently registered. Enzymatic activities were screened with possible combinations between these components, and the results indicated that Component I' of HepPS of B. stearothermophilus can be replaced by Component I of B. subtilis. The resulting hybrid-type HepPS showed some properties between B. subtilis HepPS and B. stearothermophilus HepPS, i.e. two separable components and medium heat stability. Although the subunits were not exchangeable between HexPS and the two kinds of HepPSs, some conserved amino acid residues were found among them. This implies that these residues may play an important role for the expression of the catalytic activity of medium-chain prenyl diphosphate synthases with these unique two-component systems.