The stationary asymptotic properties of the diffusion limit of a multi-type branching process with neutral mutations are studied. For the critical and subcritical processes the interesting limits are those of quasi-stationary distributions conditioned on non-extinction. Limiting distributions for supercritical and critical processes are found to collapse onto rays aligned with stationary eigenvectors of the mutation rate matrix, in agreement with known results for discrete multi-type branching processes. For the sub-critical process the quasi-stationary distribution is obtained to first order in the overall mutation rate, which is assumed to be small. The sampling distribution over allele types for a sample of given finite size is found to agree to first order in mutation rates with the analogous sampling distribution for a Wright-Fisher diffusion with constant population size.
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