The dataset presented in this article is related to the research paper titled ���Dimensional and genetic characterization of the last oriental plane trees (Platanus orientalis L.) of historical sites in Lazio (central Italy)���. Indeed, the molecular analyses reported in that article consisted in a comparison of Italian veteran plane trees with 12 certified accessions of P. orientalis , P. occidentalis and their hybrids P. acerifolia (4 individuals per species). First, LEAFY gene analyses allowed identifying 32 P. orientalis and two P. acerifolia in four sites of the province of Rome, confirming also that the two representative trees from the two gardens of the province of Viterbo belong to P. orientalis. Second, the use of Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) molecular markers provided useful information regarding the genetic relationships within and among all the historical sites. Owing to the use of SSR and ISSR molecular markers, a dataset of parameters related to the genetic diversity of the same plant material was obtained and presented in this article. For SSR markers, seven loci previously developed for P. occidentalis and two specifically developed for P. orientalis were employed. For ISSR markers, DNA samples were amplified with eight primers before used for the determination of genetic stability of micro-propagated plantlets of P. acerifolia and for the genetic characterization of plane trees within the formal gardens of Villa Lante of Bagnaia and Palazzo Farnese (Viterbo, Italy). To the best of our knowledge, this is the first report on the genetic diversity data for veteran oriental plane trees within historical sites, which will provide useful information for their management and conservation.