In the Time of the Butterflies refers to the time when the Mariposas (which is Spanish for Butterflies) were active. Mariposa is the code name that each of the three dead sisters, Minerva, Mate, and Patria, take on and use in the movement. It is also the name they were famous for. Their fellow Dominicans greeted and supported them as the Butterflies.
The novel tells about their life and times, so the title fits perfectly.