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Background  Forage species of  Urochloa  are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species ( U. ruziziensis, U. brizantha, U. decumbens  and  U. humidicola ). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in  Urochloa , where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four  Urochloa  species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels).    Results  Whole plastid genome sizes were 138,765 bp in  U. ruziziensis,  138,945 bp in  U. decumbens , 138,946 bp in  U. brizantha  and 138,976 bp in  U. humidicola . Each  Urochloa  chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses.  U. brizantha  and  U. decumbens  chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to  U. ruziziensis  and  U. humidicola . Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of  U. humidicola  from a common ancestor with the three other  Urochloa  species was estimated at 9.46 mya.  U. ruziziensis ,  U. decumbens , and  U. brizantha  formed a clade where the  U. ruziziensis  lineage would have diverged by 5.67 mya, followed by a recent divergence event between  U. decumbens  and  U. brizantha  around 1.6 mya.    Conclusion  Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of  Urochloa  used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of  Urochloa.  Our results placed the origin of  U. humidicola  and  U. ruziziensis  divergence in the Miocene-Pliocene boundary, and the split between  U. brizantha  and  U. decumbens  in the Pleistocene.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3904-2) contains supplementary material, which is available to authorized users.

Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes