The need for conservation outcomes and impact evaluations as well as reliable methods for measuring key indicators, is being increasingly emphasized worldwide. Plant height is utilized as key monitoring indicator in reintroduction and other conservation translocations and ecosystem restoration. Accurate population estimation requires careful sampling design, making it one of the most crucial steps prior to conducting research. This study was conducted to assess the nationwide distribution, population status, growth and reproductive characteristics of the endangered species Orobanche filicicola, as well as the variation in plant height within and between local populations. Additionally, it aimed to establish a monitoring framework for efficiently and reliably measuring growth indicators (i.e., plant height) necessary for evaluating the impact of conservation and recovery projects. O. filicicola was found in 7 out of 16 locations surveyed nationwide, with the population in Jeongeup being the largest in the country (N = 636). Among those sites, we selected three (two in Jeongeup and one in Jeju; total of 947 individuals) and conducted a plant height census. It revealed a height range of 3 to 50 cm, with a median of 20 cm. The Jeju population had the highest mean height (22.1±6.7cm) and the largest number of individuals per clump (median=5) among the three populations. Based on the census data, bootstrap resampling using two methods (1. Cluster sampling, 2. Two-stage sampling) showed that cluster sampling performed better in terms of variability, accuracy, and precision. Reliable population estimates were achieved when clumps were used as sampling units, and the clump sampling intensity was 60% or higher. This study highlights the importance of collecting sufficient baseline data and establishing a monitoring framework through explicit sampling design prior to conservation and recovery projects for endangered plant species.