The most recent phylogenetic hypothesis for Lepidoptera was published in Volume 2 of the "Handbook of Lepidoptera" edited by N. P. Kristensen. The first branching events in Lepidoptera are quite well documented, although there are a few contentious points still. The most problematic area of the tree is in the Ditrysia, where almost all relationships are unknown and contentious.
Inferring phylogenetic hypotheses for all of Lepidoptera has been hampered by researchers using different character sets for specific problems, both morphological and molecular. These character sets have had little or no overlap, leading to a situation where it is impossible to combine datasets for more inclusive analyses. LEPSYS.eu aims to help create standards both for morphological work and for molecular work. These standards will help guide anybody beginning to work on a previously unstudied group of Lepidoptera.
The number of gene fragments that have been used for phylogenetic studies in Lepidoptera is large. Some of the most commonly used gene regions are shown in this table:
| Gene | No. Species | Type of sequence |
| COI | 2442 | mt protein |
| COII | 959 | mt protein |
| ND1 | 281 | mt protein |
| ND5 | 350 | mt protein |
| 12S | 334 | mt RNA |
| 16S | 683 | mt RNA |
| EF-1a | 1175 | nuc protein |
| Wg | 708 | nuc protein |
As can be seen, two gene regions have been sequenced the most, the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear elongation factor-1 alpha (EF-1a). These two gene regions have been used successfully in a number of studies and are recommended as the first gene regions to sequence in any new studies. LEPSYS.eu would like to promote the use of standard molecular markers for phylogenetic studies so that we might be able to emulate the successes of the botanists, who have an extraordinary database of homologous sequences from many thousands of plant species.
Recommended priority list of gene regions to sequence in Lepidoptera:
Members of the LEPSYS.eu consortium are in the process of developing new nuclear protein-coding genes that are amplifiable from normal genomic DNA extracts. This work will be done in close collaboration with the Lepidoptera Tree of Life project in North America.
Other gene regions which have successfully been amplified from Lepidoptera:
Morphological character sets spanning more than one superfamily are as yet unavailable. Lauri Kaila (University of Helsinki) is developing such a set using characters from immatures and adults. Once this set is available, it will become the standard morphological dataset for anybody starting out on a previously unstudied group of Lepidoptera.