High mobility group (HMG)-box proteins, a large and functionally diverse superfamily of architectural protein, are involved in the regulation of DNA-dependent processes such as transcription, replication and DNA repair via the HMG-box domain. Bobby sox homolog (BBX), a newly identified HMG-Box protein, may function as a sequence-specific transcription factor. However, its expression pattern and biological functions are largely unknown. In this work, phylogenetic analysis showed that BBX is highly conserved and belongs to a novel subfamily of HMG-Box superfamily together with CIC (capicua homolog). Real time RT-PCR and whole-mount in situ hybridization in zebrafish embryo revealed that bbx, cica, and cicb were maternally highly expressed from 4 cell to 1K cell stage, and the zygote expression was primarily distributed in the central nervous system (CNS) from 24 to 60 h post-fertilization (hpf). Immunohistochemistry analysis in mouse brain revealed that BBX was weakly expressed in the cerebellum and highly expressed in the cortex and hippocampus. These findings indicate that as a novel HMG-box protein, BBX maybe associated with CNS development and provides useful clues to further study of its biological functions.