<p>Understanding the breeding practices and production systems of indigenous livestock species is essential for designing and implementing appropriate breeding strategies. This study aimed to characterize the breeding practices and production systems of indigenous goats in two agro-ecological zones of North Maluku, Indonesia: active volcanic landscapes (AVL) and crop-livestock farming (CLF). A total of 90 farmers were surveyed using semi-structured questionnaires and focus group discussions. Percentages and chi-square tests were used to identify and compare categorical variables, such as socio-economic characteristics, breeding and management practices, and housing and feeding practices across agro-ecological zones, while an index-based approach ranked farmers’ priorities regarding traits important for their production systems. Goats represented the largest proportion of livestock in the study regions. In the AVL zone, a semi-intensive management system was predominant, whereas the CLF zone primarily employed an intensive system. Farmers bred goats year-round using uncontrolled mating practices, retaining bucks born within the flock for both mating and fattening. Goats were primarily raised for income generation, savings, breeding, and religious purposes. Animals were mainly kept in separate houses from the main family house, and supplementary feeding was generally not practiced in either the AVL or CLF zones. Municipal and local aquifers served as the main water sources for livestock. Body size and growth rate were the primary criteria for selecting breeding bucks. The major diseases affecting goats included diarrhea, scabies, and pink eye, while disease, inadequate veterinary services, and insufficient veterinary drugs were the main constraints to goat production. These findings emphasize the need to strengthen farmer capacity and implement a community-based breeding program tailored to agro-ecological conditions and farmer-specific objectives to enhance genetic gains and productivity.</p>