The Supporting Information dataset included in the paper entitled Phylogenetic origin of morphologically cryptic species shapes co-occurrence and sympatry patterns includes the following files: Supporting Information 1. Species delimitation dataset: list of individuals sequenced for COI, origin of the samples, GenBank accession numbers and results of two delimitation methods. Supporting Information 2. Phylogeny dataset: list of individuals used in phylogenetic analysis with respective markers sequenced, GenBank accession numbers and geographic origin of the samples. Supporting Information 3. Niphargus rhenorhodanensis dataset: list of individuals belonging to N. rhenorhodanensis species complex, sequenced for COI, origin of the samples, GenBank accession numbers and results of two delimitation methods. Supporting Information 4. Additional information to laboratory protocols, including Table S1. Supporting Information 5. Data used in generalized model. Supporting Information 6. Figure S2: Calibrated phylogeny of Niphargus. Supporting Information 7. Table S2: A comparison of PTP and ASAP species delimitation. Supporting Information 8. Supplementary figures to results: Fig. S1: sampling locations. Figs S2-S3: rarefaction curve and distribution of MLE per clade. Figs S4-S5: distribution of pairwise sympatries with respect to time since the last ancestor and range sizes. Figs. S6-S7: Altitudinal distribution of sympatries of clades and MOTUs.