A reliable assessment of the population size of threatened species is crucial for making informed decisions about their conservation and management. However, there is a lack of comprehensive knowledge on the population of the eastern Black Crowned Crane (Balearica pavonina ceciliae), which is globally recognized as a threatened taxon experiencing a declining population trend. Here, we investigated the density, abundance and factors that influence flock size in the wetlands of the Gambella region in Ethiopia. We used line transects to collect data during dry and wet seasons. Population density and abundance were estimated using DISTANCE software, whereas factors influencing crane flock size were evaluated using a generalized linear model. We found that crane density ranged from 444 to 965 birds per sq km in the dry season and from 62 to 105 individuals per sq km in the wet season. We estimated that the population size within the designated survey areas as 7634 during the dry season and 866 during the wet season. Furthermore, for the broader survey region that encompasses permanent wetlands, the estimated population ranged from 9138 to 19,849 individuals in the dry season and from 1272 to 2166 individuals in the wet season. We found that grazing intensity and proximity to woodlands and rivers had significant positive impacts on crane flock size, whereas an increase in wetland water depth and grass height remarkably reduced flock size. As a result, wetland habitat degradation-related problems are not currently a threat to cranes in this region, but are likely to increase in the future due to large-scale agricultural expansion. The crane population size we estimated in Gambella is high, three to four times higher than the estimate from the entirety of Ethiopia. Our research underscores the global significance of Gambella wetlands as an important habitat for cranes. However, to obtain an accurate population estimate in this region, it is imperative to include seasonal wetlands, savannah grasslands, farmlands and the extended wetlands of South Sudan, which are hydrologically connected to the wetlands of Gambella region. To achieve this, comprehensive surveys and estimations should incorporate various techniques, such as aerial surveys, satellite telemetry, and high-resolution satellite imagery.