Santolina ageratifolia Barnades ex Asso is a natural autohexaploid (2n = 6x = 54, 54 + 1B), endemic to Teruel Province, Spain and inhabits a substrate derived from sandstone, red limolite and quartzite. Three chromosome formulae are found: 30m + 12sm + 12st, present in 52% of the descendants (52 metaphase), 24m + 5m-1sm + 18sm + 6st in 39% of the descendants (39 metaphase) and 24m + 5m-1sm + 18sm + 6st + 1B in 9% of the descendants (9 metaphase). Chiasmata are mostly interstitial rather than terminal, giving rise to the formation of cruciform structures. The predominance of bivalent configurations in the meiosis and the exclusively bivalent formation in four individuals indicate that this species has a strong tendency towards diploidization. Secondary association of bivalents is observed in the number of 2, 4–6 chromosomes associated, the average being 4.21 ± 1.20 chromosomes. The variation in the chromosomal characteristics suggests chromosome translocation and/or inversions. This species is partially sterile, with a mean pollen fertility of 40.56% and a mean fructification of 34.24%. The frequencies of multivalents and pollen fertility have a strongly significant effect on fructification percentage. Phenotypic variation in habits is not correlated with karyotype characteristics. The cytogeography of the polyploid taxa of the Santolina rosmarinifolia aggregate is discussed. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157, 797–807.