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Species

Citrus taxonomy is complicated and controversial. Different systems place various types of kumquats in different species or unite them into as few as two species. Botanically, many of the varieties of kumquats are classified as their own species, rather than a cultivar. Historically they were viewed as falling within the genus Citrus, but the Swingle system of citrus taxonomy elevated them to their own genus, Fortunella. Recent phylogenetic analysis suggests they do fall within Citrus. Swingle divided the kumquats into two subgenera, the Protocitrus, containing the primitive Hong Kong kumquat, and Eufortunella, comprising the round, oval kumquat, Meiwa kumquats, to which Tanaka added two others, the Malayan kumquat and the Jiangsu kumquat. Chromosomal analysis suggested that Swingle's Eufortunella represent a single 'true' species, while Tanaka's additional species were revealed to be likely hybrids of Fortunella with other Citrus, so-called x Citrofortunella.

One recent genomic analysis concluded there was only one true species of kumquat, but the analysis did not include the Hong Kong variety seen as a distinct species in all earlier analyses. A 2020 review concluded that genomic data were insufficient to reach a definitive conclusion on which kumquat cultivars represented distinct species. In 2022, a genome-level analysis of cultivated and wild varieties drew several conclusions. The authors found support for the division of kumquats into subgenera: Protocitrus, for the wild Hong Kong variety, and Eufortunella for the cultivated varieties, with a divergence predating the end of the Quaternary glaciation, perhaps between two ancestral populations isolated south and north, respectively, of the Nanling mountain range. Within the latter group, the oval, round and Meiwa kumquat each showed a level of divergence greater than between other recognized citrus species, such as between pomelo and citron, and hence each merits species-level classification. Though Swingle had speculated that the Meiwa kumquat was a hybrid of oval and round kumquats, the genomic analysis suggested instead that the round kumquat was an oval/Meiwa hybrid.