More than 90% of the carotenoids world market corresponds to chemical synthesis, but the growing demand of natural additives makes their production from microorganisms very attractive. Microalgae are one of the main sources of natural carotenoids. Although there is extensive information about the main pathways involved in the synthesis of carotenoids, the control mechanisms for this route are not clear yet. Phytoene desaturase is a key enzyme in the carotenogenic pathway. Its downregulation by homologous recombination is not possible in microalgae, in which exogenous genes are randomly inserted in the nuclear genome. Post-transcriptional silencing by antisense or inverted-repeat constructions has helped to the functional characterization of a good number of genes. Here, we show that transformation of Chlamydomonas reinhardtii with DNA encoding short hairpin RNA sequences targeting phytoene desaturase and with an antisense pds cDNA fragment causes underexpression of the target gene, but interestingly does not influence on the carotenoid profile. (C) 2008 Elsevier Ltd. All rights reserved.