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Abstract Background Diseases associated to external parasitosis are scarcely reported in sea turtles. During the last decades several organism have been documented as a part of normal epibiont community connected to sea turtles. The copepod Balaenophilus manatorum has been cited as a part of epibiont fauna with some concern about its parasitic capacity. This study serves three purposes, i.e. (i) it sheds light on the type of life style that B. manatorum has developed with its hosts, particularly turtles; (ii) it makes a cautionary note of the potential health risks associated with B. manatorum in sea turtles under captivity conditions and in the wild, and (iii) it provides data on effective treatments against B. manatorum. Results We report for the first time a massive infestation of the copepod B. manatorum and subsequent acute mortality in a group of loggerhead sea turtle hatchlings. Four-month-old turtles from a head-starting program started exhibiting excitatory and fin rubbing behavior preceding an acute onset of lethargy, skin ulceration and death in some animals. All the individuals (n = 57) were affected by severe copepod load and presented different degrees of external macroscopic skin lesions. The ventral area of front flippers, axillar and pericloacal skin were mostly affected, and were the main parasite distribution regions. Copepods were also detected on plastron and carapace sutures. The gut contents of B. manatorum reacted positively for cytokeratin, indicating consumption of turtle skin. Severe ulcerative necrotic dermatitis and large amount of bacteria presence were the major histopathological findings. Conclusions Individual fresh water immersion for 10 min and lufenuron administration (0.1 ppm) to the water system every 2 weeks proved effective for removing turtle parasites and to control re-infestation, respectively. The results from our study clearly indicated that B. manatorum individuals consume turtle skin. The pathological effects of this agent and the potential implications in sea turtle conservation and management are discussed.