Caste determination in the honeybee has been demonstrated to be decided by the royalactin in the royal jelly. And the differentially expressed coding genes in caste determination of the worker and queen larvae have also been well studied. Our experiments identified that lncRNAs are also differentially expressed in the caste determination of the larvae, which indicates that lncRNAs are involved in the caste determination. Detailed analysis showed that in the early development of the larvae, lncRNAs play a regulatory role in multicellular organismal development, nervous system development and regulation of transcription by affecting the expression and function of the nearby coding genes.