Tillandsia subgenus Tillandsia as defined by Gardner includes 269 species in five groups. Within Group I, species in the Tillandsia bulbosa complex share a remarkable synapomorphy: a pseudobulb. We sampled the 13 species of pseudobulbous Tillandsia (including T. intermedia) in addition to 18 species from the five groups of subgenus Tillandsia and four species as outgroups to perform phylogenetic analyses of sequences from two nuclear ribosomal DNA markers (ITS 2 5.8S and ETS). Three combined parsimony analyses explored the effects of indels treated as missing data, fifth character states, and with the simple indel coding method. Results show that all 13 species of pseudobulbous Tillandsia are placed within a group that also includes five non-pseudobulbous species. The pseudobulb habit is optimized as a synapomorphy for this group although with three reversals. Our analyses also show that sequence variation at ITS 2 5.8S and ETS provided resolution and indels are an important source of phylogenetic information. All previously used chloroplast markers have been shown to be almost invariant even among distantly related species in Tillandsia. Therefore, both nuclear markers assayed here are promising sources of sequence variation for reconstruction of phylogenetic relationships among species of Tillandsia and other Bromeliaceae.