Many basidiomata of the genusCandolleomyceswere found on sandy and loamy soil from the Indus Riverbed, Kot Addu District. A phylogenetic study was conducted to examine the occurrence ofCandolleomyces sindhudeltaesp. nov. using a combination of ITS and LSU regions. Our morphological, anatomical, and phylogenetic studies indicated the novelty ofCandolleomyces sindhudeltaesp. nov. The distinguishing features ofC. sindhudeltaeare convex to campanulate and areolate pileus with scalloped to cracked cap margins, branched, and pale reddish lamellae, greenish-brown ellipsoid to ovoid basidiospores, polymorphic cheilo, and caulocystidia. The novel taxa formed independent phylogenetic relationships within the genusCandolleomyces. The addition of our new species to the genusCandolleomycesmakes us confident that the genus was separated fromPsathyrellaaccurately.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02938-2.