The hippocampus plays an important role in memory formation. Hippocampal sharp wave ripples (SWRs) are critical for memory consolidation, during which a large number of hippocampal pyramidal neurons fire synchronously. Recent studies indicate that the participation of hippocampal pyramidal neurons in SWRs is variable. The variability may be explained by gene expression pattterns. However, there are no adequate methods to comprehensively analyze these molecular properties of a single neuron in the context of its electrophysiological spike patterns. Here, we developed an experimental technique to analyze gene expression profiles of a hippocampal neuron recorded under in vivo conditions by integrating existing techniques, including in vivo juxtacellular recording, cell labeling, brain slicing, patch clamping, and single-cell RNA sequencing. Using this method, we performed electrophysiological recordings and gene expression analysis of forty hippocampal CA1 pyramidal neurons. As a result of the correlation analysis between recruitment to SWRs and gene expression, we identified several genes that are potential targets for further investigation of the molecular mechanisms underlying memory consolidation. In particular, we are focusing on a gene encoding a potassium channel, Task-3 (Kcnk9). In conclusion, by taking advantage of the applicability of juxtacellular recordings in freely moving animals, our method is expected to be valuable for uncovering how spike patterns in vivo are related to the gene expression profiles of individual neurons.