Comprehensive studies of plant communities are essential for preserving rare and valuable species that are diminishing in number. Currently, there is an increasing demand for robust methodologies to conduct population-level research in geobotany, ecological monitoring, and forestry. This article focuses on the rare plant species Hepatica falconeri, Ranunculus polyanthemus L., Ranunculus oxyspermus, and Ranunculus dilatatus, which belong to the Ranunculaceae family and are found in the Tien Shan Mountains of Kazakhstan, based on geobotanical research findings. We present a manual that integrates both traditional and modern techniques for studying environmental factors, biotopes, ectopes, phytocenoses, floral composition, and the condition of natural populations of endemic and medicinal plants. This includes methodologies for assessing the biomass reserves of rare, endemic, and medicinal species, as well as evaluating the state of juvenile plants, population density, and the anatomical, morphological, phytochemical, and molecular genetic characteristics of the studied taxa. These parameters are influenced by geographical variations, microclimatic conditions, and soil properties. This article serves as a comprehensive guide for researchers in the fields of geobotany, biodiversity, botany, biology, agriculture, and medicinal plant studies. Additionally, it provides actionable recommendations for developing effective strategies for the conservation, protection, and sustainable utilization of biodiversity.