Cluster federations are attractive for executing applications like large scale code coupling. However faults may appear frequently in such architectures. Thus, checkpointing long-running applications is desirable to avoid to restart them from the beginning in the event of a node failure. To take into account the constraints of a cluster federation architecture, an hybrid checkpointing protocol is proposed. It uses global coordinated checkpointing inside clusters but only quasi-synchronous checkpointing techniques between clusters. The proposed protocol has been evaluated by simulation and fits well for applications that can be divided into modules with lots of communications within modules but few between them.