BackgroundMitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized.ResultsHere we assembled and characterized the mitogenomes of three species ofMelastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes ofM. candidum(Mc),M. sanguineum(Ms) andM. dodecandrum(Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species,M. penicillatum, which has not been fixed as it is only found in one of the three examined populations.ConclusionsBy characterizing mitochondrial genome sequences ofMelastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09488-x.