Phytopathogenic bacteria inject transcription activator-like effectors (TALEs) into plant cells to induce the expression of specific host susceptibility genes. The DNA binding specificity of TALEs is dictated by their tandem repeat regions, which are highly variable between different TALEs. We hypothesize that the unique features of the repeat regions of TALEs allow quick adaptation of the pathogens to variations of host target genes. To test this hypothesis, we utilized experimental evolution approach to mimic host adaptation of Xanthomonas citri subsp. citri (Xcc) pthA4 mutant carrying “non-adapted” TALE variants on sweet orange. We manufactured three “non-adapted” TALEs that where initially unable to induce the transcription of CsLOB1, the canker susceptibility gene, due to the presence of miss-matching repeats compared to the native CsLOB1 targeting TALE, PthA4. The TALEs were introduced into Xcc?pthA4 and bacteria were repeatedly infected and re-isolated from sweet orange plants for 32 cycles. While initially all strains failed to promote canker development, canker symptoms started to appear between 9-18 infection cycles. Sequence analysis of the adapted TALEs identified four adaptive variants, which displayed deletions and rearrangements within the tandem repeat regions of the TALEs. Reintroduction of these adapted variants into the Xcc?pthA4 restored the ability to induce the expression of CsLOB1, promote canker symptoms and colonize sweet orange plants. Our data shed light on the TALE adaptation by Xanthomonas within a host-pathogen system.