The annotated dataset of poultry diseases diagnostics for small to medium scale poultry farmers consists of poultry fecal images. The poultry fecal images were taken in Arusha and Kilimanjaro regions in Tanzania between September 2020 and December 2020 using Open Data Kit (ODK) app on mobile phones. The typical normal fecal material which is the ‘healthy’ class and Coccidiosis disease, the ‘cocci’ class were taken from poultry farms. The chickens were inoculated for Salmonella disease and fecal images taken from the diseased chickens for the ‘salmo’ class after one week. All images are in the .zip files; “cocci.zip” has 2103 images, “healthy.zip” has 2057 images, “salmo.zip” has 2276 images. A total of 6,436 image files are labeled. The “imgObjDet_Yolo.zip” and “imgSegmentation.zip” files consist of the corresponding annotations for object detection on YOLO framework and JSON files for semantic segmentation tasks respectively.