Phenylpropanoids play an important biological role in plants and are considered as potentially beneficial molecules for human health. For this purpose, they are used in pharmaceutic, cosmetic and food preparation. They are widely distributed in plants, from mosses to angiosperms but in low quantities and their extraction yield never exceeds 1% of the dry weight. Most of genes involved in the flavonoid biosynthesis pathway have been characterized and functionally expressed in recombinant microorganisms. In order to produce higher amount of flavonoids, several recombinant microorganisms have been constructed with diverse combination of flavonoid biosynthesis genes. Two expression systems, Escherichia coli and Saccharomyces cerevisiae are generally preferred for functional expressions. The use of these systems allow to synthetize up to 28 mg/l of naringenin in small-scale culture. This indicates that the two host species are promising candidates in biotechnology processes for the production of significant quantities of flavonoids. The description of the different systems used for functional expression of flavonoid genes, in regard to new developments in metabolic, genetic and process engineering constitutes the aim of this review.