Dominant selectable markers, reporter genes and regulatable systems remain powerful molecular tools for genetic and cell biology studies in fungi. Among Saccharomycotina, it is currently accepted that most species belonging to the genus Candida have adopted a specific codon usage, whereby the CTG codon encodes serine instead of leucine. This group is now widely referred to as the CTG clade. For a long time, this uncommon genetic code has precluded the use of the available Saccharomyces or bacterial markers and reporter systems for genetic studies in Candida species. Over the last 15 years, increasing effort has been made to adapt drug-resistance markers, fluorescent protein variants, luciferase and recombinase genes to favour their expression in species related to the yeast CTG clade. In addition to the growing set of Candida genome sequences, these codon-optimized molecular tools have progressively opened a window for the investigation of the conservation of gene function within Candida species. These technical advances will also facilitate future genetic studies in non-albicans Candida (NAC) species and will help both in elucidating the molecular events underlying pathogenicity and antifungal resistance and in exploring the potential of yeast metabolic engineering.