Central line associated blood stream infections (CLABSIs) in infants and children with intestinal failure due to short bowel syndrome may be caused by different organisms due to intestinal translocation and skin contamination. We report what we believe the first case of candidemia in an infant with short bowel syndrome caused by the environmental yeast Candida sojae that was initially misidentified as Candida tropicalis. We discuss its possible sources including a central venous catheter (CVC) and gut translocation and the differences between the two Candida species.