Manganese is an essential micronutrient; however, few genes required for growth under low-Mn conditions have been identified. In this study, we isolated Arabidopsis thaliana mutants sensitive to a low-Mn condition from ethyl methanesulfonate-mutagenized seeds. Among the mutants, we identified the causal genes of two mutants. One mutant (35-34) exhibited a short root phenotype and a low Mn concentration in shoots. The other mutant (30-11) exhibited a small shoot phenotype with Mn concentrations similar to the control. Genetic mapping, allelism tests, and gene complementation tests identified the causal genes, At1g80830 (NRAMP1) for 35-34, and At5g18480 (PGSIP6) for 30-11. NRAMP1 was previously reported to be essential for Mn uptake under low Mn, validating our screening method. PGSIP6 encodes inositol phosphorylceramide glucuronosyltransferase, which is involved in glycosyl inositol phosphorylceramide sphingolipid glycosylation. PGSIP6-green fluorescent protein was localized to the Golgi, which is consistent with its function in the glycosylation of sphingolipids. Our screening identified a novel gene required for low-Mn tolerance. We also provide new materials and information to understand the physiological function of PGSIP6.