The intestinal mucosa-associated microbiota could play important biological roles due to its close proximity with the animal host, but knowledge on its composition is still limited. The aim of this study was to characterize the microbial communities tightly associated with different parts (rumen, duodenum and colon) of the gastrointestinal tract (GIT) of healthy lambs and calves by using both cultural, and fluorescent in situ hybridization-flow cytometry (FCM-FISH) techniques. Lactic acid bacteria genera were one of the predominant bacteria detected in lambs and calves by both methodologies, possibly constituting an index of their healthy status. The levels of Lactobacillus were significantly higher (p<0.05) in the rumen and duodenum of lambs, and in the rumen of calves. The levels of Bifidobacterium were significantly higher (p<0.05) in the colon of both animal species and the rumen of lambs. Significant differences (p<0.05) were found in counts of other microbial groups (yeast, Enterococcus, Propionibacterium, Bacteroides, Clostridium and Enterobacteriaceae) at diverse GI sections depending on the animal species. In general, microbial counts follow the same trends regardless the applied technique. The most remarkable differences were found in detection levels of Bacteroides and Clostridium, which tended to be significantly higher (p<0.05) when analysed by FCM-FISH. This technique also allowed the detection of quantitatively important bacteria (sulphate-reducing bacteria, Atopobium and Coriobacterium), which are difficult to cultivate in selective medium. Therefore, FCM-FISH has been proven to be a sensitive high throughput approach that provides additional information to that obtained by traditional culture techniques about the complexity of the GI ecosystem of these animal species.