Artiodactyla is among the most species-rich mammalian order in Indonesia, a country known for its high level of biodiversity. However, Indonesia is also experiencing a high rate of deforestation, threatening its biodiversity, including 20 Artiodactyla species distributed throughout the country. Our goal here is to assess the status of knowledge on Artiodactyla in Indonesia to identify knowledge gaps and major biases and propose a research prospectus to stimulate new research paths and approaches. To achieve our goal, we reviewed and summarized 110 field-based research articles published between 1988 and 2022 covering Artiodactyla species throughout Indonesia and, as a comparison, Malaysian Borneo, aiming to identify biases in Artiodactyla research in the region. We found three sources of bias: 1) geographical bias, with most studies being conducted in the western part of the country and Malaysian Borneo; 2) taxonomic bias, with the number of papers covering the three most studied species equivalent to the number of papers covering the rest of the species combined; and 3) bias in research approaches, whereby few studies measured habitat selection and quality. Through our review, we provide recommendations for future research priorities, including: 1) improving research on nine understudied species, which will simultaneously add to the amount of research in less studied regions; 2) collecting basic data such as distribution and abundance for most Artiodactyla species throughout the country; and 3) integrating habitat selection assessment in designing research.