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Considerable skill is required to identify copepods at the species level based on their morphological characteristics. However, DNA analysis does not require advanced microscopy techniques and provides objective data on the phylogenetic relationships between samples. Therefore, DNA analysis is useful as an alternative method for taxonomic studies of copepods. The lysis buffer method by Lee & Frost (2002) is a simple protocol for extracting DNA from single copepod samples. In this method, a fixative, such as formalin, is first replaced with ethanol and a buffer solution. Then, the copepod sample is lysed in the lysis buffer containing a proteolytic enzyme. Thus far, we have conducted DNA extraction of single copepod samples using this method and performed gene amplification by PCR. However, due to the low success rate of PCR amplification, genetic data could not be obtained for approximately 50% of the formalin-fixed samples. In this study, we improved the lysis buffer method with the aim of enhancing the success rate of DNA extraction and PCR amplification from single copepod samples. In addition, the effect of formalin fixation time on PCR amplification was also examined.Zooplankton samples were collected from Manazuru Port, Sagami Bay on September 14, 2017, using a plankton net with a mesh size of 180 μm and fixed with 5% neutralized formalin-seawater. Adult females of the calanoid copepod Acartia japonica were selected from these samples and stored individually in ethanol. DNA was extracted from these copepods via a modified ethanol removal method, with adjustments made to the dilution of the lysis buffer, and incubation time. The mitochondrial cytochrome b gene was amplified from these DNA samples by PCR. When the concentration of the PCR product was 20 ng μL-1 or more, PCR amplification was considered to be successful. Based on the conditions optimized by the above studies, the effect of the formalin fixation time on the PCR amplification of copepods was also investigated. A higher success rate was obtained when natural drying or vacuum drying was performed to remove ethanol during DNA extraction rather than removal by pipetting. Since there was no significant difference between the results of natural drying and vacuum drying, natural drying, which is easier to perform, was selected as the optimum method. We also confirmed that a high success rate was maintained without diluting the lysis buffer after the inactivation of proteolytic enzyme. Regarding the incubation time for lysis, changing from the conventional 60 minutes to 30 minutes did not result in a significant decrease in the success rate of PCR amplification. Thus, the success rate of PCR increased to approximately 90%. Additionally, compared with the conventional lysis buffer method, the number of steps was reduced by half, and the required time was shortened from 1.5 hours to approximately 50 minutes. Furthermore, we confirmed that this improved lysis buffer method can be applied to single cells of small protozoa such as flagellates and ciliates. The effect of formalin fixation time on PCR amplification of the mitochondrial cytochrome b gene after DNA extraction via this improved lysis buffer method was investigated. As expected, the success rate of PCR amplification decreased with the formalin fixation time. However, when the fixation period was within 1 month, PCR products with a concentration of more than 20 ng μL-1 were obtained in 95% of the individual copepod samples. Furthermore, even after 3 months, similar concentrations of PCR product were obtained in 80% of individuals.Genetic analysis of small zooplankton is increasingly important not only in taxonomy but also for biodiversity and phylogeographic studies. The data presented in this study will be very important and useful in such studies.