There are several known forms of congenital erythrocytosis. Secondary forms are usually associated with increased erythropoietin levels and recognize heterogeneous genetic basis. Despite the use of NGS technologies, more than 50% of congenital erythrocytosis cases are still classified as idiopathic. Identifying the underling molecular cause appears to be crucial when a therapeutic option is available, especially if erythrocytosis is combined with progressive dysfunction of other organs. Herein, we describe the case of a patient with a rare form of congenital erythrocytosis due to bi-allelic mutations of SLC30A10 gene, responsible for a rare disease known as hypermanganesemia with dystonia 1 (HMNDYT1).