The larval stage of fish is a period of rapid morphological, anatomical and physiological transformation. The shape and structure of digestive organs is commonly used in the wild to assess the nutritional condition of larvae. However, illustrated descriptions of the ontogeny of the digestive system are rare, and non-existent for herring larvae. We studied the development of the organs of the digestive system of Atlantic herring larvae obtained from strip-spawning of wild adults (Boulogne-sur-Mer, France, November 2018) and reared under controlled condition. Larvae were reared at 13°C from hatching to developmental stage 4 (i.e. all fins present) with ad libitum feeding. The dataset contains annotated images of histological slides (sagittal sections of 7µm) of herring digestive organs throughout larval development. Two histochemical colorations were used to identify organs and mucosubstances (AB: Alcian Blue coloration; ABP Alcian Blue and Periodic acid-Schiff coloration). The dataset contains 32 files corresponding to 32 herring larvae, and a total of 221 images. The file’s name are constructed as follows: Type: Hx_Sx_xd_xmm_coloration - Hx; x is the larva number - Sx; x is the developmental stage - xd; x is the day post hatch - xmm; x is the total length in mm - AB or ABP; corresponds to the histochemical coloration used Within each folder, each image is re-identified with the larval identity “Hx” and the abbreviation corresponding to the organ(s) visible in the image. And each organ or structure is identified on the image. Abbreviation / Full name BB / Brush Border; Br / Brain; E / Enterocyte; EP / Endocrine Pancreas; Ey / Eye; F / Fin; GA / Gill Arch; GC / Goblet Cell; He / Hepatocyte; In / Intestine; Li / Liver; N / Notochord; Nu / Nucleus; O / Otolith; Oe / Oesophagus; P / Pancreas; PC / Pyloric Caecum; Py / Pylorus; SB / Swim Bladder; St / Stomach ; V / Vitellus; Z / Zymogen