These data comprise collection records of Heliconius butterfly samples collected in the Chocó-Darien ecoregion between the Andes and the Pacific in Ecuador and Colombia, and the Pacific coast of the Darien region of Panama. Samples were collected over five sampling trips between 2014 and 2016. Data were collected for a study of clinal variation across this region in Heliconius erato and Heliconius melpomene, so focus on these two species. However, in most cases all observed Heliconius species were collected. The dataset includes photographs of the wings of most of the specimens, which were used for an analysis of colour and pattern variation. Many of these individuals also have genomic information available for them on the European Nucleotide Archive (ENA) - the data includes ENA accession numbers. Data were collected as part of a NERC fellowship project (NE/K008498/1). Full details about this dataset can be found at https://doi.org/10.5285/cb23c552-caee-4221-bdd3-83b172139ae1