Observations of different molecular lines in protoplanetary disks provide valuable information on the gas kinematics, as well as constraints on the radial density and temperature structure of the gas. With ALMA we have detected H¹³CO+ (J = 4–3) and HC¹⁵ N (J = 4–3) in the HD 97048 protoplanetary disk for the first time. We compare these new detections to the ringed continuum mm-dust emission and the spatially resolved CO (J = 3–2) and HCO+ (J = 4–3) emission. The radial distributions of the H¹²CO+ and HC¹⁵N emission show hints of ringed sub-structure whereas, the optically thick tracers, CO and HCO+, do not. We calculate the HCO+/H¹³CO+ intensity ratio across the disk and find that it is radially constant (within our uncertainties). We use a physio-chemical parametric disk structure of the HD 97048 disk with an analytical prescription for the HCO+ abundance distribution to generate synthetic observations of the HCO+ and H¹³CO+ disk emission assuming LTE. The best by-eye fit models require radial variations in the HCO+/H¹³CO+ abundance ratio and an overall enhancement in H¹³CO+ relative to HCO+. This highlights the need to consider isotope selective chemistry and in particular low temperature carbon isotope exchange reactions. This also points to the presence of a reservoir of cold molecular gas in the outer disk (T ~ 10 K, R ~ 200 au). Chemical models are required to confirm that isotope-selective chemistry alone can explain the observations presented here. With these data, we cannot rule out that the known dust substructure in the HD 97048 disk is responsible for the observed trends in molecular line emission, and higher spatial resolution observations are required to fully explore the potential of optically thin tracers to probe planet-carved dust gaps. We also report non-detections of H¹³CO+ and HC¹⁵N in the HD 100546 protoplanetary disk
