Nine HII regions of the LMC were mapped in 13CO(1--0) and three in 12CO(1--0) to study the physical properties of the interstellar medium in the Magellanic Clouds. For N113 the molecular core is found to have a peak position which differs from that of the associated HII region by 20 arcsec. Toward this molecular core the 12CO and 13CO peak Tmb line temperatures of 7.3\,K and 1.2\,K are the highest so far found in the Magellanic Clouds. The molecular concentrations associated with N113, N44BC, N159HW, and N214DE in the LMC and LIRS\,36 in the SMC were investigated in a variety of molecular species to study the chemical properties of the interstellar medium. I(HCO+)/I(HCN) and I(HCN)/I(HNC) intensity ratios as well as lower limits to the I(13CO)/I(C18O) ratio were derived for the rotational 1--0 transitions. Generally, HCO+ is stronger than HCN, and HCN is stronger than HNC. The high relative HCO+ intensities are consistent with a high ionization flux from supernovae remnants and young stars, possibly coupled with a large extent of the HCO+ emission region. The bulk of the HCN arises from relatively compact dense cloud cores. Warm or shocked gas enhances HCN relative to HNC. From chemical model calculations it is predicted that I(HCN)/I(HNC) close to one should be obtained with higher angular resolution (> 30 arcsec) toward the cloud cores. Comparing virial masses with those obtained from the integrated CO intensity provides an H2 mass-to-CO luminosity conversion factor of 1.8 \times 10^{20}\,mol\,cm^{-2}\,(Kkms)^{-1} for N113 and 2.4 \times 10^{20}\,mol\,cm^{-2}\,(Kkms)^{-1} for N44BC. This is consistent with values derived for the Galactic disk
