"It must be absolutely clear," whether to refugees or those born in Germany, "that antisemitism and other prejudices have no place in our society."
"The words 'never again' have to be followed by deeds," Mrs Merkel said.
Conference participants, who attended from over 40 countries, discussed internet hate, community relations and antisemitism in sport, as well as legal, parliamentary and governmental responses to antisemitism.
Model programmes for combatting antisemitism were presented.
The conference is taking place during Germany’s chairmanship of the Organisation for Security and Co-operation in Europe (OSCE).
British delegates included Justice Secretary Michael Gove and Labour Shadow Minister Luciana Berger.