Caribe Indian tribes, Miskito and guatuzos, among other groups, were the first inhabitants of the area of the department of Rio San Juan, before they found theDesaguadero del Mar Dulce.

There are different hypotheses about the name of the municipality, one of them and the closest to reality is that provided by Ms. Felipa Beroteran, she tells us that: A turn of the century the timber from the mountains, came to rest under of Guanacaste trees, these trees were in the various hills that were characterized by abundant stones. Dona Felipa says that among the loggers call these points Morro, etc Morrito. There is the possibility that these timber which marked the beginning of the name currently held by the Municipality.

The arrival of the timber is the result of logging by American companies, and lake port characteristics facilitated the transport of timber for these companies. So too was transported to the Pacific raicilla rubber to be later exported.

Morrito Municipality, according to the law of political administrative division published in October 1989 belongs to the department of Rio San Juan.