Using reverse transcriptase-polymerase chain reaction (RT-PCR), the cDNA encoding a new isoform of the myocyte enhancer factor-2 (BMEF2) was cloned from the brain of the strain "Liangguang 2" of Bombyx mori. The open reading frame (ORF) of the new isoform shows 12 nucleotides absence of (GCACTCACAAAG) and three nucleotides mutation to the former BMEF2 (GenBank no. AB121093). Thus, we named it BMEF2B (GenBank no. EF100967). Using the SWISS-MODEL Prediction Server, the 3-D structure of BMEF2B was modeled. There are two -turns and three -helixes predicted in BMEF2B, with the pattern of -. The BMEF2B mRNA was detected not only in the central nervous system (CNS), including brain, suboesophageal ganglion (SG), thoracic ganglion (TG), and abdominal ganglion (AG), but in the non-neural tissues, such as the midgut (Mg), fat body (FB), and epidermis (Ep), muscle (Ms) and ovary (Ov). BMEF2B mRNA content in the brain was measured using the combined method of quantitative RT-PCR and Southern blotting, which kept consistently high from larvae to adults.