Long-lived radioactive krypton isotopes, (81)Kr (t1/2 = 229,000 year) and (85)Kr (t1/2 = 10.76 year), are ideal tracers. (81)Kr is cosmogenic and can be used for dating groundwater beyond the (14)C age. (85)Kr is a fission product and can be applied in atmospheric studies, nuclear safety inspections, and dating young groundwater. It has long been a challenge to analyze radio-krypton in small samples, in which the total number of such isotopes can be as low as 1 × 10(5). This work presents a system developed to analyze (81)Kr and (85)Kr from a few liters of air samples. A separation system based on cryogenic distillation and gas chromatographic separation is used to extract krypton gas with an efficiency of over 90% from air samples of 1-50 L. (85)Kr/Kr and (81)Kr/Kr ratios in krypton gases are determined from single-atom counting using a laser-based atom trap. In order to test the performance of the system, we have analyzed various samples collected from ambient air and extracted from groundwater, with a minimum size of 1 L. The system can be applied to analyze (81)Kr and (85)Kr in environmental samples including air, groundwater, and ices.