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A phylogeographic study on the chloroplast DNA of natural white oak forests (<i>Quercus</i> subgen. <i>Quercus</i>, sect. <i>Quercus</i>) was carried out to identify possible haplotype-structured distribution within the Italian Peninsula, Sicily, and Sardinia. Sixty white oak populations belonging to <i>Q. frainetto</i>, <i>Q. robur</i> and the collective groups <i>Q. petraea</i> and <i>Q. pubescens</i> were considered and analyzed by combining five Chloroplast Simple Sequence Repeat (cpSSR) markers. A total of 28 haplotypes were detected. Central and southern Italy displayed the highest variability (14 and 10 haplotypes, respectively), followed by northern Italy (7), Sardinia (7), and Sicily (5). A complex geographical structure of the haplotype distribution emerged, highlighting (i) a high number of low-frequency haplotypes; (ii) the marked isolation of Sardinia; (iii) the occurrence of haplotypes widely distributed throughout the Italian Peninsula; (iv) the idiosyncrasy of Sicily, which exhibits exclusive haplotypes, and haplotypes shared with Sardinia and the rest of the Italian Peninsula. The haplotype distribution was also found to be partially related to the taxonomic identity of the specimens, with the following features emerging: a geographic separation between the central Italy and southern Italy <i>Q. frainetto</i> populations, an unexpected discontinuity between the Calabrian and Sicilian <i>Q. petraea</i> subsp. <i>austrotyrrhenica</i> populations, and the absence of the most common haplotype among the <i>Q. pubescens</i> populations of central and southern Italy.