We characterized a new dwarf mutant with thread-like leaf, designated as thread-like leaf 1 (tll1), derived from japonica cultivar Nipponbare with ethylmethane sulfonate (EMS) treatment. tll1 was crossed reciprocally with indica cultivar Nanjing 6, Zhefu 802 and 9311. Genetic analysis demonstrated that the mutant was controlled by one recessive nuclear gene. It was mapped between two simple sequence repeat makers RM247 and RM101 on chromosome 12 in rice. Seven polymorphic sequence tagged site (STS) markers were developed from the published genomic sequences of Nipponbare and 9311. Fine mapping of the TLL1 gene located it to a 94.3-kb physical region between the STS markers FL13 and FL14, which will facilitate map-based cloning and functional analysis of the gene.