Isozyme polymorphism in leaves and seeds has been studied in 23 populations of Najas marina L. subsp. marina from Europe and the Far East, in 20 populations of N. marina L. subsp. intermedia (Gorski) Casper from Europe, the U.S.A. and Turkey and in eight populations of N. marina L. subsp. armata (Lindb. f.) Horn af Rantz. from Israel, Egypt and Burundi. These three population groups are designated as A, B and C, respectively. Alcohol dehydrogenase (ADH), glucose-6-phosphate dehydrogenase (G6PDH), glutamate dehydrogenase (GDH), isocitrate dehydrogenase (IDH), malate dehydrogenase (MDH), malic enzyme (ME), peroxidases (POD), 6-phosphogluconate dehydrogenase (6PGDH), shikimate dehydrogenase (SkDH), superoxide dismutase (SOD), xanthine dehydrogenase (XDH), glucose-phosphate isomerase (GPI) and a total protein fingerprint with sodium dodecyl sulphate (SDS) have been investigated thoroughly. ADH, IDH, ME, POD, SkDH, SOD, XDH, and GPI isozymes are polymorphic and can be used as a diagnostic tool (i.e. molecular marker) in comparing N. marina populations, while G6PDH, GDH, MDH and 6PGDH are constant in all tests. The genetic variability at 24 loci is rather low, while most of the polymorphism is mainly present in the Adh loci. Single populations seem to be very representative of their subspecies for the alleles in moderate or high frequencies. According to these isozyme patterns and the number of populations investigated here, it may be presumed that subsp. marina is very consistent for different localities in the basins of the Rivers Somme, Meuse, Mosel and Rhine (localities 1–16 and 19) but that there is a slight variation in the ADH patterns of some populations of the Alp region (Localities 17, 18 and 20), and in the SkDH pattern of those from the Far East (Localities 21–23). Subsp. intermedia, however (Localities 24–43), differs from subsp. marina, not only in a certain set of isozyme patterns, but also in the greater variation between and within populations. Allelic variants in two gene loci of ADH are detected in seed. Multiple allelic forms in the Adh-1 gene (Locus 1) are observed in plants from distant localities such as Turku, Ober-Uekersee, Kleiner Krienertsee, Gnadensee and Sempachersee (Localities 26, 32, 33, 38–40 and 41, respectively). Multiple allelic forms in the Adh-2 gene (Locus 2) are observed in plants from distant localities such as Turku, Rohr-Pöhle, Grosser Mechowsee, Faulersee, Waschsee, Gnadensee and Sempachersee (Localities 26, 34, 35, 36, 37, 38–40 and 41, respectively). A certain variation among populations is observed in ME isozymes. Subsp. armata (Localities 45–51) also differs from subsp. marina and comes very close to subsp. intermedia. Cluster analysis of electrophoretic data revealed that the exact delimitation between subsp. armata and subsp. intermedia remains difficult. The autotetraploid plants from Merkaz Sappir (Israel) occupy an intermediate position between European subsp. intermedia and the central African subsp. armata. As to the evolution of these three taxa, it is presumed that they are not derived from each other, though Karyotype A could be derived from Karyotype B and vice versa, but that they are derived from a common ancestor. The highly polymorphic subsp. intermedia and subsp. armata most likely would be closer to such a common ancestor than the subsp. marina which exhibits more genetic divergence. Enough variability is observed within the species to provide an attractive model to study and use molecular markers as a genetic basis of character correlations in its infraspecific taxa. With isozymes of N. marina L. s.l., direct information might be obtained on: the karyotype of individuals (using leaves as well as seeds); the presence of accessory chromosomes within a population (using ADH in seeds); the autotetraploid nature of individuals (using ADH in seeds) and hybrids (using ADH and ME in seeds, POD and SkDH in leaves). The investigation on natural populations reveals biogeographical patterns, such as the distribution of different alleles in ADH of the seeds. They are valuable as markers for ecodemes and in particular for the conservation of their genetic diversity.