There are unique and endemic fish species existing in freshwater ecosystems of the Troodos Mountains in Cyprus; many of which are critically endangered. The ecosystems are severely threatened by the water abstraction threats, pollution, invasive species as well as the effects of the climate change. This research is interested in the conditions of threatened fish species in Troodos Mountains with regards to their distribution, the environmental threats, and conservation priorities so as to save them. The Pseudo Phoxinus Cyprian, a critically endangered endemic species, is one of the perfect examples of how fragile these habitats are, which are limited in terms of size and also prone to water quality and availability fluctuations. Such human activities as agriculture, urbanization and also overview of non-natives such as Gambusia holbrooki, intensify these pressures and the result is habitat degradation and population declines. In reply, this study suggests a number of conservation priorities such as habitat restoration, control of invasive species and creation of protected areas. Additionally, it informs that there’s a need for scientific research, ecological monitoring as well as involving the communities in the development of effective management strategies. Preservation of these ecological system is very significant not only to ensure that the native fish species survive but also for the sustenance of ecological balance in the region. Teamwork among the governmental agencies, local communities, and scientific institutions are required to implement these strategies and sustain the freshwater habitats in the Troodos Mountains for a long time. Integrated, science-based conservation strategies are urgently needed to avert these threats to these delicate ecosystems and their biodiversity.