Biological screening of different parts of the selected Berberis species (B. brevissima Jafri and B. parkeriana Schneid) showed that methanolic root extract possessed significant efficacy against Meloidogyne javanica (a root knot nematode). From root methanolic extracts of selected Berberis species four isoquinoline alkaloids; jatrorrhizine, dehydrocheilnthifoline, berberine and berberrubine were isolated. Structures of the isolated compounds were determined by using EIMS, H-1 and C-13 NMR, and other 2D spectroscopic techniques. Percentage juveniles mortality of M. javanica was determined at various concentrations (100, 200 and 300 mu g mL(-1)) using carbofuran as control. Berberine possessed the highest nematicidal activity (71.33%) followed by jatrorrhizine (59.50%). The in vitro results suggested that these compounds from Berberis species could be potential novel nematicides against M. javanica.