The exchange of prosocial behaviors such as grooming may be affected by several factors, including the social structure and social relationships of the individuals. However, studies on the reciprocity of prosocial affiliative behaviors in non-primate animals are limited. Flipper rubbing is considered a prosocial affiliative behavior in dolphins. We investigated the reciprocity of flipper rubbing and tested the following hypotheses in common bottlenose dolphins: trade for tolerance, trade for a reduction in renewed aggressions, the value of flipper rubbing partner, and reciprocity over short and long time frames. There was no correlation between the frequency of flipper rubbing and aggression. Age difference did not affect reciprocal flipper rubbing. Flipper rubbing by former opponents did not increase after aggression. Dolphins did not provide flipper rubbing immediately after receiving flipper rubbing. The exchange of flipper rubbing was more reciprocal over long time frames than over short time frames. Dolphins preferentially rubbed the individuals who rubbed them the most. Pairs who performed flipper rubbing more frequently partook in more reciprocal flipper rubbing than pairs who performed flipper rubbing less frequently. Results suggest that bottlenose dolphins maintain flipper rubbing reciprocity over the long-term via partner choice based on an emotional bookkeeping system.