Cries were overhauled in Generation VI, so no Pokemon have identical cries -- though some are still similar sounding, particularly those related via evolutionary chains. Prior to Generation VI, there were two pairs of Pokemon with identical cries:
- Charizard and Rhyhorn
- Poliwag and Ditto
Depending on how you define "unique", you might consider Pokemon like Charmander and Charmeleon to have the same cry -- the only difference is a pitch change. Cries that were notably similar to each before (but not identical) before Generation VI include:
- Caterpie and Goldeen
- Wigglytuff and Poliwhirl
- Vileplume and Aerodactyl
- Machop and Omanyte
For more information, I recommend Bulbapedia's page on cries.