When you choose the bootstrap method for estimating the standard error, you must specify the number of replicates and the seed for the pseudorandom number generator. In each bootstrap replicate, the desired quantity is estimated and the standard deviation of the original values is computed (see Nei and Kumar [2000], page 25 for details).
It is possible that in some bootstrap replicates the quantity you desire is not calculable for statistical or technical reasons. In these cases, MEGA will discard the results of the bootstrap replicates and its final estimate will be the results of all valid replicates. This means that the number of bootstrap replicates used can be smaller than the number specified by the user. However, if the number of valid bootstrap replicates is < 25, then MEGA will report that the standard error cannot be computed (an n/c swill appear in the result window).