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Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) are two opportunistic rare yeast pathogens, which low incidence (< 1%) limits available clinical experience. Furthermore, these yeasts have elevated Minimum Inhibitory Concentration (MIC) levels to at least one class of antifungal agents. This makes it more difficult to manage their infections, and thus they are associated with high rates of mortality and clinical failure. With the aim of improving our knowledge on these opportunistic pathogens, we assembled and annotated their genomes. A phylogenomics approach revealed that genes specifically duplicated in each of the two species are often involved in transmembrane transport activities. These genomes and the reconstructed complete catalog of gene phylogenies and homology relationships constitute useful resources for future studies on these pathogens., This work received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. H2020-MSCA-ITN-2014-642095. TG group also acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BFU2015-67107 co-founded by European Regional Development Fund (ERDF); from the CERCA Program/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union’s Horizon 2020 Research and Innovation Program under the Grant Agreements No. ERC-2016-724173, and MSCA-747607. TG also receives support from an INB grant (PT17/0009/0023 – ISCIII-SGEFI/ERDF). CLF received funding from Christian Doppler Laboratory for Fungal Infections: Avoid, find, and treat! The authors thank all Gabaldón lab members for helpful discussions on this study, specially Marina Marcet-Houben., Peer Reviewed, Postprint (published version)