Robusta coffee (Coffea Canephora) is an important source of income and employment, contributing significantly to the economies of many developing countries. This species is split into two genetic groups: Guinean and Congolese. Côte-d'Ivoire is the primary diversification center of the Guinean pool, which offers great potential for genetic improvement. However, genetic erosion of this group is currently a threat in this country because of the massive introduction of Congolese accessions done in the previous decades. In this work, we analyzed the progenies of isolated population of C. canephora composed of a mix of Guinean and Congolese using SNP markers. The analysis is focus on the male parents' contribution in open pollination. The results show that the introduction of cultivars from the Congolese gene pool threat the genetic integrity of wild populations from the Guinean gene pool. Indeed, this analysis showed that Congolese pollens have more ability to pollinate the Guinean group than the Guinean pollen perform on Congolese trees. We recommend that a program be put in place to ensure the conservation of wild population of C. canephora through in situ or ex situ conservation.