Heavy metal contamination of soils is of widespread occurrence as a result of human, agricultural and industrial activities. Among heavy metals, lead is a potential pollutant that readily accumulates in soils and sediments. Although lead is not an essential element for plants, it gets easily absorbed and accumulated in Sesbania drummondii, which exhibits a significant level of tolerance to lead. The response of a metal tolerant plant to heavy metal stress involves a number of biochemical and physiological pathways. To investigate the overall molecular response of a metal-tolerant plant to lead exposure, suppression subtractive hybridization (SSH) was used to construct a cDNA library enriched in lead induced mRNA transcripts from lead-tolerant Sesbania. Screening the library by reverse Northern analysis revealed that between 20 and 25% of clones selected from the library were differentially regulated in lead treated plants. After differential screening, we isolated several differentially expressed cDNA clones, including a type 2 metallothionein (MT) gene which is involved in detoxification and homeostasis and shown to be differentially regulated in lead treated plants. The data from the reverse Northern analysis was further confirmed with conventional Northern analysis of a select group of genes including MT, ACC synthase/oxidase, cold-, water stress-, and other abiotic stress-induced genes, which are up-regulated rapidly in response to lead treatment. The mRNA levels of MT increased substantially after lead treatment indicating a potential role for it under lead stress in Sesbania. The present results show that SSH can serve as an effective tool for isolating genes induced in response to lead heavy metal tolerance in Sesbania. A better understanding of lead induced gene expression in Sesbania should help select candidates associated with remediation of heavy metal toxicity. The possible link between this result and the heavy-metal response of plants is discussed.