The dataset contains 219 entries with 241 records of specimens from the families Limoniidae, Pediciidae and Tipulidae, collected between 1985 to 2019 in continental Portugal (Oosterbroek et al., 2020, part). All specimens have been identified to species level, in a total of 65 species representing 45% of the craneflies known for continental Portugal. Specimens were collected in 67 different localities. The dataset “Diptera 03 - Further records on Portuguese Limoniidae, Pediciidae and Tipulidae” is part of a group of DNA barcoding datasets of Diptera conducted within the InBIO Barcoding Initiative (IBI), two of which have already been made available through GBIF (“The InBIO Barcoding Initiative Database: Diptera 01”, https://doi.org/10.15468/q1bvt3; “The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae”, https://doi.org/10.15468/f6256w). IBI is funded by the EnvMetaGen and PORBIOTA projects. Most specimens (142) are deposited in the IBI collection. Other specimens are deposited in the Collection Rui Andrade (Porto, Portugal, 76 specimens), the Hunterian Zoology Museum (Glasgow, U.K., 22 specimens) and in the Naturalis Biodiversity Center, Zoology collections (Leiden, Netherlands, 1 specimen).