Coffea genus (Rubiaceae), recently increased to 110 species, is divided into two subgenera: Coffea subgenus Coffea (101 species), native mainly to Africa and the Indian Ocean islands and Coffea subgenus Baracoffea (nine species), restricted to Madagascar. To date, genome size data are available for only 25 species, mainly of African origin. The aim of this study, using flow cytometry on lyophilized material, was to assess the genome size of 44 species natives to the Indian Ocean islands and to investigate its correlation with biogeography, leaf traits and phylogenetic relationships. The mean 2C nuclear DNA content of Mascarocoffea species ranged about 1pg to 1.40 pg. The overall 2C DNA values from African and Indian Ocean islands species were non-linearly distributed. A geographical map according to the putative native origin of the corresponding species showed a gradient in Madagascar and Africa. Genome sizes increased following a North to South-East gradient in Madagascar and an East to Central-West gradient in Africa. No, or only weak, correlations were noted between genome size and leaf parameters. Genetically close species could be highly distinctive in their genome size while divergent species could be similarly sized. The non-random geographic distribution and habitat of species, and the absence of correlation between genome size and genetic relationships, suggested that during Coffea genome evolution both DNA content increase and/or decrease occurred independently in Africa and in the Indian Ocean Islands.