Thaliaceans are gelatinous holoplanktonic tunicates comprised of around 72 described species in three orders: the Pyrosomatida (pyrosomes), Salpida (salps) and Doliolida (doliolids). Despite their interesting biology and important role in ocean ecosystems, relatively little is known about their evolutionary relationships with other tunicate lineages and with each other. Here, using 40 newly obtained 18S rDNA sequences, we present a molecular phylogeny of the Thaliacea. Our results show the pyrosomes branching off first and support their division into the Pyrostremmatinae and Pyrosomatinae. Within the Salpida, we found the subfamily Salpinae is paraphyletic with the morphologically divergent Cyclosalpinae. We also resolved the uncertainty regarding Weelia (Salpa) cylindrica, finding it to be relatively distantly related to Salpa aspera, Salsa maxima, Salpa fusiformis and Salsa thompsoni.