In this study, Vitis vinifera, Prunus persica and Theobroma cacao were selected as the research objects.Based on the comparative genomics, the genomic structure and gene homology information were comparatively analyzed by homologous genes collinearity method to determine homologous fragments within and between selected genomes. The statistics of the retention of homologous collinear genes among three species genomes showed that Vitis vinifera genes retained the best, followed by Prunus persica better (about 73.4%) and Theobroma cacao came last (about 68.9%), all of which could be due to common triploidization of dicotyledons leading to the destruction of genomic stability. In addition, the frequency distribution of synonymous nucleotide substitution rates between collinear homologous genes indicated that Vitis vinifera, Prunus persica and Theobroma cacao genomes had only experienced an ancient whole-genome triploidization without other whole-genome polyploidization recently. It was found that Theobroma cacao genome evolved most fastly andVitis vinifera evolved most conservatively. The differentiation time of three species were also estimated that Vitis vinifera (~110 Mya), Theobroma cacao (~90 Mya) and Prunus persica(~80 Mya). This study would provide important theoretical basis for researches on genomic structure, function and evolution of three species and dicotyledons.