In the past few decades, nanometer-scale pores have been employed as a powerful tool for sensing biological molecules. In pursuit of this technology, a variety of nanotechnology-based approaches have been explored and established, especially nanopore sequencing. In comparison to the existing pores in other materials such as Si3N4, carbon nanopores have the ability to rapidly sense various biological molecules at single-molecule resolution and with reduced cost. Different from most reviews about nanopore sequencing, herein, we focus on the nanopore materials employed for sequencing applications. Initially, we provide an overview on the general issues associated with nanopore sequencing, concentrating on the recent progress and achievements in nanopore sequencing, especially using various carbon nanomaterials such as graphene and carbon nanotubes. Finally, the future research directions using carbon nanomaterials for nanopore sequencing are discussed and outlined.