Significant variations of nanomechanical properties and fracture morphology between gene-mutated liliput(dtc232) (lil/lil) zebrafish skeletal bone and wild-type bone have been observed. Nanoindentation measurement disclosed that lil/lil bone has 36% lower nanohardness and 32% lower elastic modulus. The standard deviations of hardness and elastic modulus of lil/lil bone were both much higher than those of wild-type bone. SEM morphology of fracture surfaces further revealed that in bones after gene mutation, formative microcracks make the performance reduction and the increasing of brittleness. What is more, the plywood-like structure of the normal bone does not exist in the lil/lil bone.