Genetic investigation of wild primates are crucial to understand kinship, population diversity, phylogeographic patterns, and heritable factors of phenotypes. Traditional DNA technology using polymerase chain reaction (PCR) and Sanger sequencing have restricted the genome-wide analysis of primates, particularly due to the low quality and low quantity of noninvasive DNA samples obtained from wild individuals. Following the post-genome era, next-generation sequencing (NGS) technologies have provided a new paradigm in primate studies. NGS has enabled the genome-wide analysis of primate DNA using noninvasive samples, such as feces. Metabarcoding and metagenomics analyses using fecal samples provide information on food items and commensal microorganisms of the host animal. Here, I review a history of DNA sequencing technologies and examples of NGS studies in wild primates. Further, I discuss the effectiveness of NGS application to noninvasive samples.