Effects of non-adjacent character repetition were investigated using the same-different matching task. We compared matching of strings of 5 consonants with matching of 5 symbols in order to distinguish letter-specific mechanisms from generic order encoding mechanisms. Character repetition was found to facilitate “same” responses to both types of stimuli, but crucially the interfering effect of repetition on “different” responses was only significant with letter strings. However, the latter effect only emerged in response times (as well as error rates) when the repetition occurred in the target string as opposed to the reference string. We conclude that inhibitory effects of letter repetition reflect the operation of a letter-specific order encoding mechanism, and that letter repetition in the target string has a greater influence than letter repetition in the reference string when making “different” responses in the same-different matching task.