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Kaplan Z. & Fehrer J. 2004: Evidence for the hybrid origin of Potamogeton ×cooperi (Potamogetonaceae): traditional morphology-based taxonomy and molecular techniques in concert. Folia Geobotanica 39, 431 - 453.
Kaplan Z. & Symoens J.-J. 2004: Proposal to conserve the name Potamogeton schweinfurthii A. Benn. (Potamogetonaceae) with a conserved type. Taxon 53, 837 - 838.
Kaplan Z. & Wolff P. 2004: A morphological, anatomical and isozyme study of Potamogeton ×schreberi: confirmation of its recent occurrence in Germany and first documented record in France. Preslia 76, 141 - 161.
Kaplan Z. & Zalewska-Gałosz J. 2004: Potamogeton taxa proposed by J. F. Wolfgang and his collaborators. Taxon 53, 1033 - 1041.
Prausová R., Husák Š., Kaplan Z., Adamec L. & Rybka V. 2004: Řešení záchrany poslední populace rdestu dlouholistého (Potamogeton praelongus Wulfen) v České republice. (.) Ochrana přírody 59, 82 - 86.
Pyšek P. & Kaplan Z. (eds.) 2004: Botanické studie věnované památce Emila Hadače / Botanical studies dedicated to the memory of Emil Hadač. Preslia 76, 193 - 290.
Kaplan Z. & Štěpánek J. 2003: Genetic variation within and between populations of Potamogeton pusillus agg. Plant Systematics and Evolution 239, 95 - 112.
Kaplan Z. 2002: Phenotypic plasticity in Potamogeton (Potamogetonaceae). Folia Geobotanica 37, 141 - 170.
Kirschner J. & Kaplan Z. 2002: Taxonomic monographs in relation to global Red Lists. Taxon 51, 155 - 158.
2002: Mandák B. & Pyšek P. (2002): Reynoutria, křídlatka. – In: Kubát K., Hrouda L., Chrtek J. jun., Kaplan Z., Kirschner J. & Štěpánek J. (eds.), Klíč ke květeně České republiky, p. 201–202, Academia, Praha..
2002: Mandák B. (2002): Atriplex, lebeda. – In: Kubát K., Hrouda L., Chrtek J. jun., Kaplan Z., Kirschner J. & Štěpánek J. (eds.), Klíč ke květeně České republiky, p. 181–183, Academia, Praha..
Kirschner J. & Kaplan Z. 2001: Proposals to reject the names Juncus cymosus, J. radicans, Luzula capillaris, L. hyperborea, L. interrupta, and Rostkovia brevifolia (Juncaceae). Taxon 50, 1193 - 1197.
Kirschner J. & Kaplan Z. 2001: Taxonomic and nomenclatural notes on Luzula and Juncus (Juncaceae). Taxon 50, 1107 - 1113.
Kirschner J., Novara L. J., Novikov V. S., Snogerup S. & Kaplan Z. 1999: Supraspecific division of the genus Juncus (Juncaceae). Folia Geobotanica 34, 377 - 390.