This study intends to reliably estimate the general status of the benthic and the epiphytic foraminifera community related to each studied seagrass ecosystem (Posidonia oceanica, Cymodocea nodosa and Halophila stipulacea) distributed in different shallow sites in the coastal archipelago of Kerkennah (Gulf of Gabes, Tunisia) during winter. We were able to first sort and subsequently identify some characteristics conditioning their behaviour. Twenty-four species of foraminifera were encountered. Among them, three epiphytic species identified on these seagrass leaves had a much lower abundance than those in the sediment. We were interested in highlighting the foraminiferal community related to Halophila stipulacea, since this seagrass species is newly introduced into the Mediterranean sea. Thanks to the statistical study, we were able to identify the favourable habitat for epiphytic and benthic foraminifera among the three seagrass ecosystems. A correlation between the identified foraminifera species and some environmental parameters was addressed using a variety of software.