This study presents the historical background and details of the Kyoto Protocol, its flexible mechanisms, and carbon markets. As the carbon market appears to be the most visible result of regulatory efforts to mitigate climate change, this study provides comprehensive reviews of the operation of the European Union Emissions Trading Scheme (EU ETS), the Clean Development Mechanism, the Joint Implementation and also other segments of the global carbon market. It appears that the existing several carbon markets mostly operate in isolation from each other, which leads to a fragmented global carbon market. This analysis suggests that improving the competitive conditions of carbon markets and increasing the substitutability of project-based credits for allowances can develop the integration of the markets. Potential improvements may include providing greater availability of credits within the EU ETS, providing greater clarity and simplicity of the EU ETS’s rules regarding the use and the import of project-based credits, providing greater coordination between the EU ETS and the Kyoto mechanisms, and providing greater harmonization in regulatory frameworks.