Legumes are second only to cereals in their importance to humans, and study of their functional genomics of nutrition and other trace elements is crucial for agricultural production and food fortification. We describe here an ionomic screening experiment carried out to investigate the accumulation of 15 elements in shoots of mutants of Lotus japonicus, a good genetic tool for legume study.Approximately 2000 mutagenized M2 plants were cultivated in a novel low-cost high-throughput system and their elemental profiles were determined by inductively coupled plasma mass spectroscopy (ICP-MS).After triple-checking the element concentrations in M2 or M3 plant shoots, 31 mutants with altered elemental profiles were identified. Surprisingly, the number of genes regulating essential elements was similar to the number regulating nonessential elements. Magnesium (Mg) and nickel (Ni) were correlated in a number of mutants.Further investigation suggested that phosphorus (P) and cobalt (Co) might be involved in the ion homeostasis network of Mg and Ni.The results suggested that the pathways for element uptake or translocation were highly linked through the ion transport-related genes. Ionomics proved to be a powerful functional genomics tool for determining genes related to ion homeostasisin this study.