The chancellor, in her weekly podcast, said those who had challenged the former communist regime from within - people involved in citizen groups and the democratic opposition to the communist regime - had "demonstrated courage".
"They gave courage to others," she said, particularly the hundreds of thousands who participated in the "Monday demonstrations" in Leipzig and across other East German cities, whose actions shook the regime's rulers.
Without them, she said, "this process would have been much more difficult... this is why we must say a big thank you".
A former citizen of East Germany herself, Merkel also spoke of the "indescribable feeling" at the fall of the wall on November 9th, 1989.
She said that she spent the beginning of that evening in a sauna with a friend before heading out to one of the many demonstrations. "The feeling can never be forgotten," she said. "It has changed lives."
Twenty five years on from the fall of the wall, structural differences still remain, especially when it comes to employment and Merkel said that many in the east had at first struggled to find employment when Germany was reunited.
However, she said the "new generations are now welded" to modern Germany and thanks to the "incredible support" of those in the west of the country, the gap had been closed.
Germany will celebrate the 25th anniversary with a number of festivities, including several concerts close to Berlin's famous Brandenburg Gate.
SEE ALSO: How Berlin has changed since Wall fall