Token-based flow control of messages in a parallel computer, the parallel computer including a plurality of compute nodes, each compute node including one or more computer processors, including: allocating, by a token administration module to a plurality of the computer processors in the parallel computer, a number of data communications tokens; identifying all communicators executing on each computer processor, where each communicator is participating in a distinct parallel operation executing on the parallel computer; allocating, to the communicators, the data communications tokens; determining, by a communicator attempting to send data to the destination, whether the communicator has enough available data communications tokens to send the data to the destination; and responsive to determining that the communicator has enough available data communications tokens to send the data, sending, by the communicator, the data to the destination.