Date palm (Phoenix dactylifera L.) is mainly cultivated for its edible fruit and is of great socio-economic importance for the populations of arid zones. Analysis of the date palm genetic diversity in the Old World had revealed a strong genetic structure with the existence of two gene pools, one Eastern comprising Asia and Djibouti, and one Western, consisting of North African accessions. So far, mainly date palm populations from countries within the Maghreb and the Middle East were characterized, but no information from the Sahel was included. Here, we present the genetic diversity of date palms from Southeastern Niger. The DNA of 113 date palm accessions were analyzed and compared with a database containing the genetic information of 248 accessions from the Old World. The diversity generated from microsatellite markers was compared to that of the same loci of both the Eastern and Western genetic pools. Our results show that date palms from Southeastern Niger constitute a unique group with a high level of genetic diversity. Moreover, even though this group is included in the Western genetic pool, it shows a specific originality which differentiates it from other Western populations. It also shows one of the lowest admixture levels of the Western pool. Global analysis showed a secondary genetic structure within the Western pool highlighting a new genetic group located in Southeastern Niger that distinguishes itself from the North African group.