SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally . Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19 . The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain . In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols . Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages . All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change . The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region . Three sequences were assigned to the new B.1.1.7 lineage . Our work is an important contribution to the understanding of the epidemiology of SARS- CoV-2 in Ecuador and South America.