Isopentenyl diphosphate(IPP) isomerization to dimethylallyl diphosphate(DMAPP) is an important step for the efficient production of isoprenoids such as lycopene, β-carotene, astaxanthin, etc. The type Ⅱ isopentenyl diphosphate isomerase gene from Synechocystis sp. PCC6803(sll1556, Syidi2) was cloned and expressed in Escherichia coli DH5α. When E. coli DH5α harboring lycopene synthesis genes, crtE, crtB, and crtI and mevalonate pathway genes, MvK1, MvK2, and Mvd, was cultured on LB medium containing mevalonate, the strain grew very slowly be due to the toxicity of isopentenyl diphosphate derived from mevalonate. When Syidi2 was introduced to E. coli DH5α harboring the lycopene synthesis genes and mevalonate pathway genes, growth on mevalonate medium was fully restored and the colony showed red color indicating lycopene formation. The growth rate of the mutant strain, E. coli DH5α(idi::Δkm), was very slow because of IPP accumulation and DMAPP deprivation. Ultimately the idi mutant was complemented by introducing the Syidi2 gene.