Traditionally, applications that are used in large and small enterprises were deployed on “bare metal” servers installed with operating systems. Recently, the use of multiple virtual machines (VMs) on the same physical server was adopted due to cost reduction and flexibility. Nowadays, containers have become popular for application deployment due to smaller footprints than the VMs, their ability to start and stop more quickly, and their capability to pack the application binaries and their dependencies/libraries in standalone units for seamless portability. A typical container ecosystem includes a code repository (e.g., GitHub) where the container images are built from the codes and libraries and then pushed to the image registry (e.g., Docker Hub) for subsequent deployment as application containers. However, the pervasive use of containers also leads to a wide-range of security breaches such as attackers stealing credentials, source codes and sensitive data from image registry and code repository, carrying out DoS attacks on application containers, and gaining root access to misuse the underlying host resources, among others. In this paper, we first perform threat modeling on the containers ecosystem using the popular threat modeling framework, called STRIDE. Using STRIDE, we identify the vulnerabilities in each system component, and investigate potential security threats and their consequences. Then, we conduct a comprehensive survey on the existing countermeasures designed against the identified threats and vulnerabilities in containers. In particular, we assess the strengths and weaknesses of the existing mitigation strategies designed against such threats. We believe that this work will help researchers and practitioners to gain a deeper understanding of the threat landscape in containers and the state-of-the-art countermeasures. We also discuss open research problems, the research gaps and future research directions in containers security, which may ignite further research to be done in this area.