Aims. To explore the nature of the unidentified very-high-energy (VHE, E > 100 GeV) gamma-ray source HESS J1626−490, we investigated the region in X-ray, sub-millimeter, and infrared energy bands. Methods. So far only detected with the HESS array of imaging atmospheric Cherenkov telescopes, HESS J1626−490 could not be unambiguously identified with any source seen at lower energies. Therefore, we analyzed data from an archival XMM-Newton observation, pointed towards HESS J1626−490, to classify detected X-ray point sources according to their spectral properties and their near-infrared counterparts from the 2MASS catalog. Furthermore, we characterized in detail the diffuse X-ray emission from a region compatible with the extended VHE signal. To characterize the interstellar medium surrounding HESS J1626−490 we analyzed 12CO(J = 1−0) molecular line data from the Nanten Galactic plane survey, H i data from the Southern Galactic Plane Survey (SGPS) and Spitzer data from the GLIMPSE and MIPSGAL surveys. Results. None of the detected X-ray point sources fulfills the energy requirements to be considered as the synchrotron radiation counterpart to the VHE source assuming an inverse-Compton (IC) emission scenario. We did not detect any diffuse X-ray excess emission originating in the region around HESS J1626−490 above the Galactic background and the derived upper limit for the total X-ray flux disfavors a purely leptonic emission scenario for HESS J1626−490. We found a good morphological match between molecular and atomic gas in the −27  km s-1 to −18 km s-1 line-of-sight velocity range and HESS J1626−490. The cloud has a mass of 1.8 × 104   M⊙ and is located at a mean kinematic distance of d = 1.8 kpc. Furthermore, we found a density depression in the H i gas at a similar distance, which is spatially consistent with the SNR G335.2+00.1. We discuss various scenarios for the VHE emission, including the CO molecular cloud being a passive target for cosmic ray protons accelerated by the nearby SNR G335.2+00.1.