Rare earth elements (REEs) are metallic elements with electronic, magnetic, optical and catalytic properties which make them essential in many industrial and medical fields. REEs are therefore becoming emerging pollutants and it is important to understand their implications for ecosystem health. However, little knowledge of REE bioaccumulation in aquatic organisms is available and especially on their internal distribution in fish. In the present study, REE organotropism was determined in Anguilla anguilla from the Loire estuary (France) by determining burdens in a wide set of tissues, organs and biological fluids. Differences have been observed between life stages and genders. For yellow eels, the most accumulating organ was the gills (126.90 ± 50.78 μg/kg dw) and for silver eels, it was the liver (181.78 ± 62.04 μg/kg dw for males; 203.79 ± 111.86 μg/kg dw for females). The comparison between female silver and yellow eels shown that female silver individuals accumulated significantly more REEs in the urinary system (US), muscles, gonads, spleen and liver, while yellow individuals accumulated more in gills. The comparison between male and female silver eels also highlighted differences, indeed the females accumulated significantly more REEs in the US, gonads, skin and spleen, compared to males which accumulated significantly more in muscles and gills. REEs abundances are also different between organs, life stages and genders. The gonads of female silver eels exhibited a particular profile with the dominance of gadolinium (Gd) (up to 74.2% of ∑REEs). Moreover, the presence of Anguillicola crassus in the swim bladder of organisms seemed to have an impact on REE bioaccumulation: parasitized yellow eels present higher concentrations of REEs in muscles, gills, gonads and liver than non-parasitized individuals. Regarding glass eels, REE contribution profiles in the whole body were close to those of yellow and silver eel skin.