Puccinellia fasciculata is a littoral miohalophyte with a Mediterranean-Atlantic distribution, uncommonly found in inland sites. The main Italian inland population is located in the "Salse di Nirano" Reserve, an area internationally renowned for the phenomenon of mud volcanoes. In this study, molecular markers are used to characterize this population and its possible relationships with the nearest littoral conspecific population. A survey of ISSR markers revealed low levels of genetic diversity (He = 0.081 in the inland population, 0.105 in the littoral one) and a weak genetic differentiation (Gst = 0.24 within the inland population, 0.28 among this and the littoral one). A sequence analysis of three non-coding regions of chloroplast DNA found no genetic differentiation both within the inland population and between the two populations, and revealed a common origin for the two dating back to the middle Holocene. The apparent incongruence between the results from the two approaches may be explained by differences between ISSR and non-coding cpDNA markers in capturing signatures related to gene flow; their integrated information implies a mixed reproductive strategy and a common evolutionary history for the two examined populations. Effective conservation strategies are recommended for the inland population of P. fasciculata and its habitat.