<p>Background: Coenzyme Q10 (CoQ10) is an isoprenoid component used widely in nutraceutical industries. Farnesyl diphosphate synthase (FPPS) is a responsible enzyme for biosynthesis of farnesyl diphosphate (FPP), a key precursor for CoQs production. This research involved investigating the effect of FPPS over-expression on CoQs production in engineered CoQ10-producing Escherichia coli (E. coli).<br /> Methods: Two CoQ10-producing strains, as referred to E. coli Ba and E. coli Br, were transformed by the encoding gene for FPPS (ispA) under the control of either the trc or PBAD promoters.<br /> Results: Over-expression of ispA under the control of PBAD promoter led to a relative increase in CoQ10 production only in recombinant E. coli Br although induction by arabinose resulted in partial reduction of CoQ10 production in both recombinant E. coli Ba and E. coli Br strains. Over-expression of ispA under the control of stronger trc promoter, however, led to a severe decrease in CoQ10 production in both recombinant E. coli Ba and E. coli Br strains, as reflected by reductions from 629&plusmn;40 to 30&plusmn;13 and 564&plusmn;28 to 80&plusmn;14 &micro;g/g Dried Cell Weight (DCW), respectively. The results showed high level of FPP reduces endogenous CoQ8 production as well and that CoQs are produced in a complimentary manner, as the increase in production of one decreases the production of the other.<br /> Conclusion: The reduction in CoQ10 production can be a result of Dds inhibition by high FPP concentration. Therefore, more effort is needed to verify the role of intermediate metabolite concentration and to optimize production of CoQ10.</p>