Marine zooplankton has important ecological and economic value. The observation and automatic image recognition technology of marine zooplankton is an important mean to acquire data such as species, quantity, spatial distribution and behavioral postures of zooplankton, and is an important support for marine scientific research. Digital holography has an innate advantage of refocusing and reconstruction, which is suitable for deep learning and living zooplankton recognition. In this study, a large number of holographic images was trained by using the improved YOLOv2 model, and after test, the study achieved satisfactory results: the models trained by the images with sharpness assessment score of 0.6 or higher, have precision rate above 94% and a recall rate above 88%. This study mainly discusses: (1) the detection method of moving targets to acquire the images of moving zooplankton; (2) the two factors that affect the holographic images recognition results, mean (pixel mean of images) subtraction operation and image sharpness, and the no-reference sharpness assessment based on structural similarity for holographic images; (3) the relationship between sharpness assessment index or mean subtraction and the recognition results.