The livestock farming especially dairy industry is among the important components of the livestock sector in Zanzibar in terms source of animal protein, income, and employment. The present study was meant to investigate milking hygiene and handling practices among smallholder dairy farmers in Zanzibar. Cross-sectional study was conducted whereby a structured questionnaire was addressed to 359 dairy cattle farmers. The assessment of milking hygiene and handling practices among smallholder dairy farmers on were analyzed and then judged based on the selected indicators of good dairy farming practices of FAO and International Dairy Federation (IDF) and IDF, (FAO, 2011) and Zanzibar Food and Drug Board standard. The results revealed low milking hygiene and good handling practices. In addition, based on the Zanzibar Food and Drug Board’ standards, farmers comply lowly with milk quality standards and food safety regulations. It was also found that farmers, traders and processors practised milking hygiene and handling measures like hand washing, udder and utensils cleaning milking boiling and packaging. However, key un-hygiene practices include the use of plastic containers, untreated water, and lack of teat dipping. It is recommended that, for safe and quality milk availability, farmers must be equipped with knowledge and skills on good milking hygiene and handling practices. There is a need to improve farmers’ knowledge and implement hygienic milking practices in the milk production process to meet required milk quality and food safety standards. In addition, awareness creation on the importance of good milking and handling practices will create behavioural change and lead to an improvement in milk quality in Zanzibar.