The considerable decline in wild populations of the sea cucumber Isostichopus badionotus in the Yucatán Peninsula has been driven principally by overfishing and illegal harvesting. Consequently, aquaculture has been developed as an alternative to commercial fishing and as a strategy for the restoration of natural populations. Nevertheless, the emergence of various health issues, such as a larval disease and the skin ulceration syndrome (SUS), in juveniles has limited the success of its cultivation under controlled conditions. This study analyzed changes in the intestinal and skin microbiota of cultured juveniles during an outbreak of SUS. Juvenile I. badionotus were obtained from an experimental culture in Telchac Puerto, Yucatán, during a SUS outbreak. Samples of intestinal and skin tissues were processed for histological examination and 16S rRNA gene sequencing to characterize microbial communities. Histological analysis revealed that apparently healthy juveniles exhibited tissue alterations compatible with an early stage of SUS. Intestinal inflammation was detected in both stages of disease. However, severe epithelial damage and bacterial clusters were only observed in juveniles in the advanced stage of SUS. Microbiota analyses revealed significant differences in bacterial composition, particularly in the intestine, with a marked decrease in Vibrio and an increase in Halarcobacter (syn. Arcobacter), suggesting a dysbiosis process during disease progression. These findings highlight the complex microbial dynamics underlying SUS and emphasize the importance of microbiota monitoring for effective health management in I. badionotus aquaculture.