Our understanding of how molecular clouds form in the interstellar medium ( ISM ) would be greatly helped if we had a reliable observational tracer of the gas flows responsible for forming the clouds . Fine structure emission from singly ionised and neutral carbon ( [ CII ] , [ CI ] ) and rotational line emission from CO are all observed to be associated with molecular clouds . However , it remains unclear whether any of these tracers can be used to study the inflow of gas onto an assembling cloud , or whether they primarily trace the cloud once it has already assembled . In this paper , we address this issue with the help of high resolution simulations of molecular cloud formation that include a sophisticated treatment of the chemistry and thermal physics of the ISM . Our simulations demonstrate that both [ CI ] and CO emission trace gas that is predominantly molecular , with a density n \sim 500 –1000 cm ^ { -3 } , much larger than the density of the inflowing gas . [ CII ] traces lower density material ( n \sim 100 \ > { cm ^ { -3 } } ) that is mainly atomic at early times . A large fraction of the [ CII ] emission traces the same structures as the [ CI ] or CO emission , but some arises in the inflowing gas . Unfortunately , this emission is very faint and will be difficult to detect with current observational facilities , even for clouds situated in regions with an elevated interstellar radiation field .