Abstract: Pepper is one of the important vegetable crops and condiments in China. Carrying out researches on pepper genomics is of great significance for understanding the genetics and evolution of peppers, tapping important functional genes of peppers, and using biotechnology to conduct genetic improvement of varieties. The release of the draft pepper genomic map in 2014 marked the entry of pepper into an era of genomics research. Over the past decade, remarkable progress has been made in pepper genomics research, revealing the basic features of pepper genome deeply and constructing a preliminary pan-genome of pepper. Meanwhile, pepper genomics has been widely applied in exploring the interspecific differentiation and gene introgression of pepper, analyzing the evolutionary mechanism of pepper important traits, elucidating the genetic diversity of pepper, revealing the characteristics of artificial domestication of pepper, tracing the history of global range expansion and dissemination of pepper, and exploring the genes controlling the formation of important traits of pepper and so on. In this paper, we review and summarize the progress made in pepper genomics and its applications over the past 10 years, and look forward to the construction of a higher-quality pepper reference genome and pan-genome as well as the improvement of the research platform for pepper functional genomics, with an aim to provide a reference for pepper genomics and related applications.