Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Most probiotic microorganisms used in the food industry are strains belonging to the genera Lactobacillus and Bifidobacterium, and the most common vehicles to deliver them include dairy products such as fermented milk or yogurt. In these products, the bacteria can contribute to the food fermentation or just be present as adjunct culture. However, the natural habitat of probiotics is normally the intestinal tract of humans and mammals. Therefore, the capacity of these bacteria to adapt to the food environment is critical in order to deliver the microorganism in a physiological state that allows survival and, desirably, persistence and colonization of our gut epithelium. In this way, the study of novel markers and traits related to probiotic robustness is of key importance to avoid a low bacterial viability. In this chapter, we attempt to shed some light on the strategies to make a rational selection of Lactobacillus and Bifidobacterium strains intended to be used in functional foods, as well as the processes to enhance their functionality.