The subgeneric subdivision of the genus Formica is still open. In this article, we make a phylogenetic study on several species of the genus Formica and of its closely related genera, Polyergus and Proformica, using sequences of nuclear satellite DNA (stDNA) and the mitochondrial rrnL as molecular markers. Our goal was to shed light on their phylogenetic relationships and particularly on the systematic position of F. subrufa. This species was first included in the subgenus Serviformica, but afterwards a new subgenus (Iberoformica) was established to include only this species. The results show that a stDNA family previously reported in Formica species, with a repetitive unit 129 bp long, is also found in Polyergus rufescens and P. samurai but not in Proformica longiseta. This is the first case of presence of a stDNA family in two different ant genera. In F. subrufa, this stDNA is very divergent relative to those isolated in the remaining Formica species and in the genus Polyergus. The Bayesian analysis of mitochondrial rrnL sequences shows three highly supported groups: F. subrufa, the remaining Formica species studied, and the genus Polyergus, suggesting that parasites (Polyergus species) and hosts (Formica species) are closely related but not sibling species. The combined analysis of nuclear stDNA sequences and mitochondrial rrnL showed their phylogenetic congruence despite their distinct evolutionary dynamics. This analysis did not discriminate between the remaining Formica species that were not grouped according to the subgeneric classification. According to these results, it can no longer be assumed that F. subrufa belongs to the subgenus Serviformica or of the fusca species group. This differentiation was also supported by previous studies based on the morphological characters, molecular and cytogenetic data. Therefore, taking into consideration these arguments and others explained in detail in this article, we propose that the taxon Iberoformica, formerly synonymized subgenus, be raised to a genus status. This genus would be monotypic and only composed, up to the moment, by Iberoformica subrufa (= F. subrufa Roger, 1859).