Konrad Adenauer, Ludwig Erhard, Kurt Georg Kiesinger and Helmut Kohl were CDU chancellors without SPD for a total of 36 years. Merkel had one election period out of four without SPD, so there was a total of 40 years of no SPD. That is much longer than "almost never" for a country that is about 80 years old.
There were SPD chancellors for 24 years total, CDU the rest. German politics have been traditionally mostly CDU dominated.