Specimens of Bertiella studeri (Cyclophyllidea, Anoplocephalidae) that have been preserved in ethanol or fixed permanently in formalin for >2 years were used for DNA extraction and molecular characterization. DNA was amplified via PCR from samples collected from different monkey and human hosts using eucestoda-specific primers. Phylogenetic trees were inferred from two sets of sequence data corresponding to the first and second halves of the 18S rDNA gene using two methods (distance-based NJ and maximum parsimony). We found that the second dataset was more suited for inferring phylogeny within the Cyclophyllidea. Both trees show that taxa belonging to the Anoplocephalidae, Hymenolepididae, Davaineidae, and Mesocestoididae are clearly monophyletic within their families and demonstrate sister-group relationships between the Anoplocephalidae and Mesocestoididae, contradicting previous reports of a basal placement of the Mesocestoididae within the Cyclophyllidea. The distance-based phylogeny support a taxonomical classification that groups members of the Bertiella genus, as well as other members of the Anoplocephalidae family, as being most closely related to the Hymenolepididae family and can be used to substantiate the use of uterine morphology as a valid homologous trait for taxonomical and phylogenetic classifications. On the other hand, the parsimony-based phylogeny places the Hymenolepididae closer to the outgroup and shows a closer relationship between the Mesocestoididae and the Taeniidae. This underlies the caution with which gene trees should be interpreted for inferring phylogeny and underlies the need to integrate both morphological and molecular data to represent the actual evolutionary pathway of the species involved.