Hyperhydricity was observed throughout in vitro multiplication phase of a Eucalyptus grandis clone. Ultrastructural approach of tissue and cell differentiation, izoenzyme patterns, binding protein (BiP) expression, and pigment content were performed. Hyperhydric tissues showed a reduction in cell wall deposition, reduction of membranous organelles, higher cell vacuolation, and more intercellular spaces than its normal counterpart. Additionally, several vesicles were present in hyperhydric cells suggesting the occurrence of organelle autophagy by autophagic vacuole. Lower pigment content, intercellular spaces on the epidermis and the induction of a molecular chaperone (BiP) were observed in hyperhydric phenotype. Evidences of schizolysigenous process of intercellular space formation are compatible with a stress condition. Although plastoglobulli were observed in normal and hyperhydric chloroplasts, they were more evident in the normal ones. Abnormal stomata also reflected a disruptive situation and morphogenesis disturbances which would difficult plant acclimatization. Further observation of the epidermis ultrastructure allows us to conclude that the presence of intercellular spaces on its surface may be constraining the recovery and development of hyperhydric plants. Similarly to BiP, other proteins such as esterase (EST), acid phosphatase (ACP), malate dehydrogenase (MDH) and peroxidase (PDX) are possible to be used as stress markers in in vitro conditions. Our results confirm earlier findings about negative effects of hyperhydricity on in vitro plant morphogenesis and ultrastructure, which in eucalypt is associated with a stressful condition contributing to lower propagation ratios.