Honeybee diseases are one of the most significant and most common causes of honeybee colonies' weakness and death. An early diagnosis of subclinical infections is necessary to implement precautionary and control measures. Sampling debris from hive bottom boards is simple, non-invasive, and cheap. In this study, we collected winter debris samples in apiaries located in the continental part of Croatia. We used molecular methods, PCR and qPCR, for the first time to analyze those samples. Laboratory results were compared with the health condition and strength of honeybee colonies at an apiary in spring. Our study successfully identified the presence and quantity of various pathogens, including the presence of spp. ( spp.), quintefied , Acute Bee Paralysis Virus (ABPV), Black Queen Cell Virus (BQCV), Deformed Wing Virus (DWV), and Sacbrood Virus (SBV). However, our analysis did not detect , , , and . Samples of winter debris were also examined for the presence and quantification of the mites, and their natural mite fall was observed in spring. Honeybee colonies were simultaneously infected by an average of four to six pathogens. Some observed honeybee colonies developed characteristic symptoms, while others did not survive the winter.