A genomic clone encoding the mouse lysosomal alpha-mannosidases was isolated and the gene was found to be encoded by 24 exons spanning approximately 14.5 kb of genomic DNA. The intron-exon boundaries were conserved between the mouse, human, and bovine lysosomal alpha-mannosidase genes as well as being partially conserved in several other species. In order to define the promoter of the mouse mannosidase gene, >1 kb of DNA sequence was obtained upstream from the respective initiation codon. The transcription start site was identified by a 5'-RACE procedure and putative promoter elements were identified by expression of promoter/reporter constructs. Fluorescence in situ hybridization analysis using the mouse and human mannosidase genomic clones as probes, localized the mouse gene to chromosome 8, at band position 8C2, and the human gene to chromosome 19p13.2, a region syntenic to the lysosomal mannosidase gene on mouse chromosome 8.