Kopyor coconut (Cocos nucifera L.) is one of the most valuable crops in Indonesia because of its paramount interest. Indeed, this type of coconut is very sought after by Indonesian buyers for a high price because of their limited production. However, there are some limitations and constraints for the large-scale plantation especially on producing true-to-type kopyor coconut, neither availability of genetic diversity information nor ex situ conservation has been developed. Moreover, Banyumas as one area with the highest diversity of kopyor coconut is almost forgotten in Indonesia.  A study on genetic diversity of kopyor coconut in two regencies, Banyumas and Purbalingga, has been made using morphological and molecular approaches. The results revealed that Purbalingga regency has more kopyor diversity compared to Banyumas regencies. Even though both tall and dwarf kopyor have been found in the two areas, the diversity of kopyor in Purbalingga was richer than its neighbour based on morphological analysis using 15 principal components analysis.  A microsatellite analysis using ten molecular markers on two normal and two kopyor coconuts also showed a high diversity among coconut coming from those two regencies. Later, we proposed to develope a very first seed genebank of kopyor in Indonesia.