[Objectives]  To identify and analyze virulence factor-related full-length transcripts of Ascosphaera apis, a lethal fungal pathogen that exclusively infects honeybee larvae causing chalkbrood disease, using previously gained high-quality long-read sequencing data, thereby providing reference information and a foundation for the functional study of virulence factor-associated isoforms of this pathogen. [Methods]  All full-length transcripts of A. apis mycelium (AaM) and spores (AaS) were aligned to the Nr database using BLAST tool to identify full-length transcripts relative to virulence factors, such as chitinase, lipase, hydrolase and protease. Sequences of full-length transcripts in AaM and AaS were aligned to those of known transcripts annotated in the A. apis reference genome, followed by normalization of the numbers of full-length transcripts mapped to the reference genome. The expression levels of each virulence factor-related, full-length transcript were then calculated. A heatmap showing the spatial pattern of transcript expression was drawn using the appropriate tool in BMKCloud and the structures of partial virulence factor-related full-length transcripts were visualized in IGV browser. [Results]  367 genes and 407 full-length transcripts associated with virulence factors were identified in AaM, of which 12 were chitinase-related, 48 lipase-related, 289 hydrolase-related and 58 protease-related. 367 genes and 400 full-length transcripts associated with virulence factors were identified in Aas, of which 14 were chitinase-related, 63 lipase-related, 267 hydrolase-related and 56 protease-related. In addition, there were 0 and 17 unique virulence factor-related, full-length transcripts（lipase-related and chitinase-related transcripts）in AaM and Aas, respectively, and 60 that were common to mycelia and spores. Further analysis indicated that part of the virulence factor-related genes can generate several isoforms via alternative splicing. [Conclusion]  A total of 367 genes and 486 full-length transcripts associated with virulence factors, such as chitinase, lipase, hydrolase and protease were identified. Most full-length transcripts corresponding to virulence factor-related genes were relatively abundant and had more complex structures. Our findings enrich the annotation of genes and transcripts relevant to Ascosphaera apis virulence factors, provide a foundation for the functional study of virulence factor-associated isoforms and offer potential targets for the prevention and control of chalkbrood in honey-bees.