Although there have been advances in acid-suppressive medications and eradication of Helicobacter pylori (H. pylori), peptic ulcer disease (PUD), is still a major gastrointestinal disorder worldwide. This polyetiology, including its oxidative stress, inflammatory, mucosal defence and apoptotic and delayed tissue repair mechanisms, has motivated the search for new gastroprotective agents, including those derived from natural sources. Experimental animal models are critical in testing these agents; selection of a biomarker is of paramount importance for a good assessment of gastroprotection. Along with the traditional macroscopic and gastric secretory parameters, recent studies have increasingly used oxidative stress, inflammatory and cytoprotective biomarkers as well as molecular ones to explain the mechanism of gastric mucosal damage and defence. The present review gives a summary of the status of the use of biomarkers in experimental peptic ulcer models, their biological significance, analytical method, advantages and limitations. It also covers new biomarkers discovered via transcriptomics, proteomics, metabolomics and digital pathology, as well as standardization and reproducibility and clinical translation. Finally, future perspectives emphasizing integrated biomarker panels and advanced analytical technologies are presented. In this review, a brief overview is given on the selection and interpretation of biomarkers for experimental studies of gastro-protection and their usefulness to the development of better anti-ulcer drugs.