Advances in fecal DNA technology have expanded its usages in molecular ecology, especially in genetic assessment of wild animals. The technology allows researchers to understand ecological issues without contacting, disturbing, or even seeing animals, thus avoided invasions to the animal studied, and greatly promotes studies in molecular ecology of wild animals. Although this technology could yield poor DNA and relatively high genotyping errors in its early stages, these problems have been overcome gradually with the technological achievements being made in the past 25 years. Nowadays, fecal DNA technology yields good DNA and low genotyping errors, allowing researchers to address questions in reliability. Here, we share our knowledge about technological pitfalls on fecal sampling, preservation, DNA extraction, PCR, and genotyping in detail, and discuss opportunities and challenges of its applications, aiming to increase the power and role of the technology in molecular ecology of wild animals.