Merauke Regency is the largest area in Papua Province and includes potential in the livestock sector. Regional potential analysis based on leading livestock population aims to provide regional information based on livestock sector potential, which can be used as information in policy making in government programs. A hybrid algorithm combining LQ and complete linkage can map potential livestock areas based on leading populations. The results of the LQ analysis show that there are six leading types of livestock: cows, buffaloes, horses, kampong chickens, laying chickens, and ducks. The leading livestock types can be used as a source of information regarding regional potential in the livestock business and classified into four clusters. The clustering of regional potential using a complete linkage hierarchical algorithm with a livestock population dataset by conducting four trials and yielding information that Semangga and Tanah Miring sub-districts have potential in the livestock sector. The proposed method used a hybrid approach to analyze the potential of livestock areas in Merauke and determine the leading types of livestock in the area to classify areas in each cluster and map the potential of livestock areas using GIS techniques.