The genus Lasiodiplodia, a member of the family Botryosphaeriaceae, is an important fun-
gal disease genus in agriculture. However, the Lasiodiplodia species survey and genetic diversity in
Taiwan remain unclear. This study aimed to investigate the Lasiodiplodia species associated with
various fruit species to explore the cryptic Lasiodiplodia species diversity, validate species delimita-
tion, and unveil cryptic genetic diversity. Overall, six Lasiodiplodia species were identified, with sev-
eral new records of infection identified. Additionally, phylogenetic analyses indicated that the rela-
tions of all isolates of L. theobromae might be paraphyletic. They were grouped with L. brasiliense
based on Automatic Barcode Gap Discovery (ABGD), Automatic Partitioning (ASAP) and struc-
ture-based clustering analyses. These analyses did not provide conclusive evidence for L. brasiliensis
as a stable species. It may be nec sary to gather more information to clarify the species delineation.
The multiple new records of Lasiodiplodia species with high genetic diversity and differentiation
revealed that the diversity of Lasiodiplodia in Taiwan was underestimated in the past. We found that
L. theobromae has the highest number of haplotypes but the lowest number of haplotype and nucle-
otide diversities, indicating a recent population expansion. This was supported by the significant
negative Tajima's D and Fu and Li's D* tests. The high genetic diversity, low gene flow, and host-
associated differentiation of Lasiodiplodia species indicate that they might harbour powerful evolu-
tionary potential in Taiwan. This study provided critical insights into genetic variation, host-asso-
ciated differentiation, and demography of Lasiodiplodia species, which would be helpful for disease
management of related pathogens.
