This is a range-restricted species, known from three sites on the island of Kithira, making it rare in Greece. Its area of occupancy (AOO) is 12 km². It is considered to occur at three locations and the quality of its habitat is declining as a result of tourism and road construction. In the first edition of the Red Data Book of the Rare and Threatened Plants of Greece, it was assessed as a Vulnerable taxon, due to its restricted distribution and its small population (Phitos and Iatrou 1995). Later, in 2005, its extinction risk status changed to Critically Endangered, based on the IUCN Criteria B1ab(iii)+2ab(iii) (Montmollin and Strahm). Given the restricted distribution and population size of this species, ongoing monitoring of population trends and threats is required, alongside a more thorough evaluation of current threatening processes. As the species is not known to occur within any protected areas, and its survival is considered to rely upon protection of its habitat, site protection and habitat restoration represent essential conservation measures. Education of landowners about the threatened status of this species is also recommended. Since there are two new sites that have expanded the area of occupancy (AOO) and extent of occurrence (EOO) of the species since the previous, it is assessed here as Endangered under criterion B1ab(iii)+2ab(iii).

This species is endemic to Kithira, a small Greek island of 284 km² which lies opposite the eastern tip of the Peloponnese, Cape Malea, in the Ionian Sea. The taxon was known from a population near Kalamos village (Phitos and Iatrou 1995, Montmollin and Strahm 2005), but it was also found in other sites on the island, by Yannitsaros (2004). It is difficult to find not only because it is rare, but also because it is rather inconspicuous.

Stefi et al. (2023) researched the population of the species and found in the area of Myrtidia a subpopulation between 116 and 200 individuals. It is impossible to exactly identify the individuals among the “nursing” plants. Their measurements were restricted in the area near the unpaved road, as it is difficult to penetrate on foot into the dense vegetation of Genista and Sarcopoterium. In the area of Kalamos, they counted more than 200 individuals and in the area of Vroulea, the team detected a decrease in the subpopulation there. In 2022, they had counted 86 individuals and in 2023, there was a maximum of 50 individuals, due to the significant degradation of the area. The researchers noted a dried vegetation throughout the area; dry shoots of Genista, Erica, Pinus, Thymus composed a degraded landscape, but despite the adverse conditions, cachectic shoots of Polygala were spotted struggling to survive.

This perennial herb grows on sandy soil and rarely occurs in open areas. Usually its slender branches can be seen protruding from spiny cushions composed of other plant species growing in the same vegetation type. Poylgala helenae has a narrow ecological range. It usually grows in association with Spiny Broom (Genista acanthoclada) and Thorny Burnet (Sarcopoterium spinosum) which typically characterise "phrygana" vegetation. This vegetation type is composed largely of spiny or aromatic dwarf shrubs, growing in lowland areas on dry soils. In Greece there are several types of phrygana, depending upon grazing pressure, the incidence of fires, exposure, soils and geology. A crimson tulip, the Greek endemic Tulipa goulimyi, may also be found growing in the same areas as P. helenae (Phitos and Iatrou 1995). According to Yannitsaros (2004) and Stefi et al. (2023), in the two new localities the plant is rare, growing in phrygana dominated by Sarcopoterium spinosum, Genista acanthoclada, Coridothymus capitatus, Calicotome villosa, Erica sp., Cistus sp. and low shrubs of Pistacia lentiscus. The species grows between or under these shrubs and is easily overlooked. Related species are Polygala venulosa and P. supina, which are Balkan endemics (Montmollin and Strahm 2005).

The natural habitat of P. helenae was once cultivated. While the area is no longer used for agriculture, there is an increasing risk that it may be needed for agricultural purposes again. Should this happen, then the species would probably disappear. Increased tourism also poses a threat to this plant (Montmollin and Strahm 2005). Furthermore, fire is another major threat to the species. According to Stefi et al. (2023), another problem for the distribution of the species in Vroulea is that it is growing on the existing unpaved road. It is rumoured that the widening of the road and its cement-paving is about to happen in the near future. In addition, this area has not been affected by wildfires for over a hundred years, which means it might be easily be burned in the future. On the other hand, despite the landscape degradation and population decline, the sight of many ants carrying ripe seeds of Polygala, which had fallen on the dirt road, gives hope for the future of the plant; seed dispersal by ants (myrmecochory) in Polygala species is already known due to the well-developed seed elaiosomes. Furthermore, the presence of Apis sp. nectaring on P. helenae, sheds optimism on the future of this hallmark plant of the island.

This species is included in national legislation (Presidential Decree 67/1981), however no measures have been taken yet. It is also included in the Top 50 Mediterranean island plants on the brink of extinction (Montmollin and Strahm 2005). Ex-situ cultivation from seeds and attempts to transplant this species from the wild into the Botanic Garden of the University of Patras have both failed (Phitos and Iatrou 1995). Stefi et al. (2023) collected 600 mature and immature seeds for their ex-situ conservation goals (i.e. scientific research and long-term storage in our Seed Banks - National and Kapodistrian University of Athens and the Millennium Seed Bank Kew) within the framework of a satellite assignment to the “Conserving the Flora of the Balkans: Native Plants of Greece” Project”. If the ex-situ conservation efforts become unsuccessful, it would seem that the best option to conserve this species is to protect and manage the area where it is known to occur. More fieldwork on Kithira is also needed to see if this species might occur in other areas and research must be continued for the entire population of the species, in order to effectively protect it, as well as for its ecology, the threats it faces in every locality and actions that must be taken towards its conservation. Monitoring the population for several years along with planning its recovery and management of the area it occupies, must go on. Citizens' awareness and communication of the significance of this plant for the country's environment will also play a huge role for its survival.