The conservation of citrus seeds is limited in time because they lose their germination capacity after few months at 20 °C. A broad evaluation of the seed desiccation tolerance was carried for 41 varieties from the main species of Citrus, Fortunella and Poncirus genus. Seed Water Content (WC) and fruit size are relevant indicators for assessing the optimal maturity of seeds prior to processing. Seed water content and temperature are key factors in sensitivity to desiccation. After 30 days at 25 °C, seeds undergo accelerated ageing at varying rates depending on the species. Water exchange between seeds and the atmosphere varies depending on the genus. It is lower in Poncirus trifoliata, leading to higher seed moisture content than in varieties of the Citrus species. Trifoliate oranges and kumquats are very sensitive to desiccation and the WC50 threshold (50% of germination loss) is high (around 28%), and their germination is null at 20% of WC. Citrons (C. medica) and their relatives, limes and lemons, are highly tolerant to low WC (<6%) and so they seed could be considered as orthodox. Grapefruit and pummelo seeds are medium tolerant while mandarin and sweet orange seeds are sensitive to 12% WC. This study is a preamble to the seed preservation of citrus germplasm because it allows the adaptation of drying protocols to each species and indicates the improvements needed for partially sensitive species.