Molecular evidence favors three major metazoan clades, Deuterostomia, Ecdysozoa and Lophotrochozoa, each of them containing one major segmented animal taxon (e.g. Annelida in Lophotrochozoa). Thus, segmentation is more widely dispersed than previously expected. However, it still remains uncertain if segmentation is plesiomorphic for Bilateria or at least Protostomia or whether it evolved independently several times. A central part in resolving this issue is the position of Annelida within Lophotrochozoa and the affiliation of unsegmented taxa like Echiura and Sipuncula to Annelida. Furthermore, Lophotrochozoa as well as Annelida represent an important part of the marine biodiversity, but their phylogenies are still unresolved. Unfortunately, the vast of amount of molecular data to date (August 2006) is concentrated on a few model species (e.g. Homo, Mus, Drosophila, Caenorhabitis ) and eventually their allies (e.g. 33 genome projects within the genus Drosophila). On the other hand, only 5 projects in Lophotrochozoa are listed in NCBI GenBank (done, assembly or in progress). The same could be shown for EST databases.

The first multi-gene analysis comprising up to 11 nuclear and mitochondrial genes within Annelida shows that Echiura is sister to Capitellidae and Sipuncula most likely an annelid subtaxon. Therefore, annelid segmentation is much more variable than previously considered. Furthermore, both homonomous segmented Amphinomidae and heteronomous Chaetopteridae occupy basal positions in the tree. Additionally, Clitellata are also certainly a subtaxon of polychaetes synonymizing "Polychaeta" with Annelida.

However, the sister groups of Sipuncula, Clitellata and Siboglinidae within Annelida as well as the relationship of Annelida to other lophotrochozoan taxa such as Mollusca, Kamptozoa and Nemertea has still to be determined. Other topics within Lophotrochozoa are also unresolved and in need of further data mining, e.g., affiliation of Platyzoa to Lophotrochozoa, or relationships of lophotrochozoan taxa to each other. The problematic phylogeny of lophotrochozoan taxa is addressed within the DFG special program "Deep Metazoan Phylogeny - Stammesgeschichte der Großgruppen der Tiere" project DFG-STR-683/3-1 "Phylogenetic position of Annelida and possible subordinated taxa (e.g. Sipuncula) within Lophotrochozoa based on molecular data" using multi-gene as well as phylogenomic approaches (i.e. EST databases).