Bryozoans are a moderately diverse, mostly marine phylum with a fossil record extending to the early Ordovician. Compared to other phyla, little is known about their phylogenetic relationships at both lower and higher taxonomic levels. Hence, an effort is being made to elucidate the phylogenetic relationships among bryozoans. Here, we present newly sequenced nuclear and mitochondrial genes for 21 cheilostome bryozoans and compile these with existing orthologous molecular data. Using these data, we focus on reconstructing the phylogenetic relationships of Fenestrulina and Microporella, two species-rich genera. They are currently placed in a globally distributed family, Microporellidae, defined by having a semicircular primary orifice and a proximal ascopore, although there are indirect inferences in the morphological literature that suggest they might not be confamilial. Our six-gene phylogenetic analysis reveals that the genera Fenestrulina and Microporella are each monophyletic, with the sister clade to Microporella comprising non-microporellids. These genera thus have a polyphyletic relationship and should not be placed in the same family. Our result supports the reinstatement of the family Fenestrulinidae Jullien, 1888 for Fenestrulina and genera with comparable frontal shield and ooecial morphologies. Our well-supported phylogeny based on independent molecular data lends credit to existing phylogenetic hypotheses based on morphological observations but does not conform to the current classification of these particular bryozoans. This illustrates the general need for a rethink of bryozoan higher-level systematics, ideally based on both morphological and molecular data.