To understand alterations of oxalate and other metabolite levels induced by aluminium ion (Al3+) stress in Rumex plants, we measured the metabolites in R. obtusifolius using the capillary electrophoresis–mass spectrometry. Oxalate and its precursors (isocitrate and citrate) accumulated in leaves of R. obtusifolius after the Al3+ treatment at pH 4.5. Such increase was not observed under the acidic condition (pH 4.5) without Al3+. Principal component analysis showed organ-specific changes in metabolite levels in R. obtusifolius by the Al3+ treatment. Highly positive correlations between oxalate and its precursors were revealed by hierarchical clustering and correlation analyses. An increase in oxalate content was consistently observed for three Rumex species (R. obtusifolius, R. crispus and R. japonicus) grown in the presence of Al3+. On the other hand, multivariate analyses revealed the differential alterations of other metabolite levels between R. obtusifolius and the other two Rumex species.