Cycloalkanes are hydrocarbon compounds commonly present in crude oil and condensate, and they are degraded in the marine environment mostly by low-temperature microorganisms. Most of these microorganisms are difficult to culture in the laboratory, and therefore the majority of the active species involved in marine cycloalkane degradation have not been identified yet. This study used a combination of stable isotope labeling, single-cell Raman sorting technology, and 16S rRNA gene sequencing to discover a new genus of uncultured marine bacteria, C1-B045, that can effectively consume methylcyclohexane (MCH) in the marine environment. We used RACS-Seq^® to link metabolic phenotype and genotype at single-cell resolution, and proposed an ε-caprolactone MCH degradation pathway. This pathway may involve multiple key enzymes, including alkyl monoxygenase, cyclohexanone monoxygenase, and 6-caprolactone hydrolase.