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In Tunisia,Thymus algeriensisoccurs in small scattered populations decreasing progressively in size. However, no conservation programs are attempted to promote and preserve the potential value of this resource. In this work, we assessed the genetic diversity of 21 populations ofT. algeriensiscollected from different geographical regions using nine isozyme systems. Fourteen polymorphic loci were detected and several ones were rare alleles according to population level. The species showed a high genetic diversity within populations (Ap = 2.25;P% = 75.71%;Ho = 0.151). A relatively high level of differentiation (FST = 0.146) associated with a restricted gene flow among populations (Nm = 2.385) was revealed. A significant population differentiation (0.055 < FST < 0.183) was observed within ecological groups. The relationship betweenFSTand geographic distance matrices was not significant, indicating that the genetic structure among populations is more linked to fragmentation of populations. Nei's genetic distances (D) among pairs of populations were low (0.005 < D < 0.126). The substantial differentiation between populations and their high genetic similarity suggest their recent divergence as a result of habitat fragmentation and isolation of populations. UPGMA clustering showed four aggregates according to their geographic and bioclimatic originality. Theex situconservation should be based on sampling seeds within rather than among populations. [ABSTRACT FROM AUTHOR]