The innovation of colonizing the marine environment came at the cost of losing large gene blocks, which can promote structural or numerical chromosome changes for seagrasses. To understand (1) what events shaped the karyotype of this ecological group, and (2) what the implications of this evolutionary route are, the present study presents a reconstruction of the ancestral chromosome number of marine angiosperms. Phylogenetic reconstruction was inferred under a Bayesian approach using a matrix combined with the ITS1−5.8S-ITS2, matK and rbcL markers of 46 seagrass species. Reconstruction of the ancestral haploid chromosome number was implemented in ChromEvol 2.0 and dating in Beast 2.3.2. Our phylogenetic inference showed that the five families investigated formed four clades, and the currently accepted separation between Cymodoceaceae and Ruppiaceae is not supported (pp = 0.8). The reconstruction indicated n = 10 as the ancestral number at the base of the marine angiosperms, which is maintained in 18 species (± 39 % species) distributed in 3 of the 4 families, except in Hydrocharitaceae. The main events that led to the evolution of the karyotype of marine angiosperms were fusion and duplication, with fusion the major contributor and most frequent in the internal branches of phylogeny. A greater number of species derived from dysploidy was verified when compared to species derived from duplication, resulting from the natural difficulty of stabilizing neopolyploids.