A set of 867 COSII markers allowed to established macrosynteny between coffee, tomato and grapevine. Coffee and tomato genomes shared 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine shared a similar number of syntenic markers (299) and CSSs (29). Despite important genome macrostructure reorganization, several large chromosome segments showed exceptional macrosynteny, shedding new insights into chromosome evolution between flowering plants. In addition, we analyzed a BAC sequence of 174 kb containing the Ovate gene, conserved in a syntenic block between the three plants, that showed a high microsynteny conservation. Surprisingly, a higher level of conservation was observed between coffee and grapevine, both ligneous and perennial plants, than between coffee and tomato, an annual plant. Out of 16 genes identified in coffee on this segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. A significant conservation was found at the macro- and micro-structure levels between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades. Conservation did not decline at the Ovate locus in relation to phylogenetic distance, suggesting that the time factor alone does not explain all the divergences. These results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy.