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Fallacia is distinguished morpho‐anatomically from Navicula sensu lato based on the possession of an H‐shaped chloroplast, lateral sterna and a finely porous conopeum, but whether this genus is monophyletic is still in question. Three new Fallacia species are described based on morphology and SSU rRNA and rbcL gene sequences: Fallacia tateyamensis sp. nov., Fallacia bosoensis sp. nov. and Fallacia laevis sp. nov. We performed the first comprehensive molecular and morphological phylogenetic analyses of 31 Fallacia species based on 11 new sequences from six species and 23 morphological characters. We also documented the detailed morphogenesis of Fallacia for the first time. Fallacia is not monophyletic. Both morphological and DNA sequence data supported the separation of Rossia from Fallacia, while the phylogenetic position of Pseudofallacia is uncertain. We recognized four morphogroups in Fallacia by morphological and molecular phylogenetic analyses. Ancestral character reconstruction indicated that diatoms in Sellaphoraceae evolved from the possession of two lateral narrow parallel depressions covered by narrow nonporous conopea, to lyre‐shaped canals covered by wide porous conopea. Lanceolate canals and the presence of areolae in canals evolved multiple times independently. [ABSTRACT FROM AUTHOR]