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BACKGROUND: Ecuador is a country working towards elimination of malaria since 2012. The number of malaria cases decreased by more than 99% since 2001. Nevertheless, in recent years the progress has stagnated, and the number of cases has remained constant or increased in some areas. One of the main difficulties for the elimination of malaria in Ecuador is migration from neighboring countries. More than 75% of Plasmodium falciparum cases are concentrated in the north coast of the country near the border with Colombia.METHODS: With the goal of contributing to epidemiological surveillance in Ecuador by characterizing the P. falciparum parasites circulating in the country, the present study focused on parasites collected in northwest Ecuador to identify the possible origin of P. falciparum currently circulating. We collected 72 clinical samples between 2019 and 2021 in three localities of northwest Ecuador as well as samples originating from the bordering Nariño department in Colombia that were diagnosed in Ecuador. We performed an analysis of seven microsatellite markers and whole genome sequencing (WGS) and compared them to previously studied parasites from the region to measure their relatedness as identity by descent (IBD).RESULTS: Our results show shared, highly clonal parasites between Ecuador and Colombia. All infections were monoclonal. Most importantly, a low frequency clone previously found circulating in the Pacific Coast of Colombia but not in Ecuador caused new outbreaks through clonal expansions. This clone had high genetic differentiation with parasites previously circulating in the Pacific Coast of South America.CONCLUSION: This study confirms the persistence of long-term clones in the Pacific Coast of South America and demonstrates the potential importance of low prevalence clones to become epidemic and hamper elimination efforts in low transmission areas.