Several Canalisporium species collected from freshwater habitats in Taiwan are described and illustrated. These include six new species and four new records for Taiwan, namely, C. caribense, C. elegans, C. jinghongense, C. kenyense, C. macrosporum sp. nov., C. nanhuaense sp. nov., C. parvum sp. nov., C. paulopallidum sp. nov., C. taiwanense sp. nov., and C. waffleum sp. nov. Based on a re-examination of the type specimens, the placement of C. nigrum in Canalisporium was verified, but C. microsporum was found to be previously misidentified. The latter was renamed as Trimmatostroma canalisporioides. Other Canalisporium species not collected in Taiwan are briefly discussed. The phylogenetic relationship of Canalisporium species was sought among representative taxa from related fungal familiar lineages, namely, the Conioscyphaceae, Fuscosporellaceae, Pleurotheciaceae, and Savoryellaceae, by comparing the sequences of their nuc rDNA ITS1-5.8S-ITS2 (ITS barcode). Identification of Canalisporium species accepted in this paper is based on phylogenetic relationship and morphological comparison, plus some statistical analyses. A key to the 21 accepted species of Canalisporium is given. A composite diagram of conidial morphology of these species is provided to ease identification. Separation of Canalisporium species into two major groups based on conidial morphology with phylogenetic support is discussed.