Through an integrative approach that combined microscopy and molecular analyses of the 18S rDNA gene, this study describes a novel haemococcidian species, Lankesterella nucleoflexa sp. nov., and presents data on another Lankesterella sp. Both parasites were found in the green iguana (Iguana iguana) from Eastern Amazonia, Brazil. Lankesterella nucleoflexa sp. nov. is characterized by a unique nuclear plasticity; its nucleus exhibits variable shapes and condensation states, appearing condensed and seemingly divided when adjacent to the host cell nucleus and elongated when positioned opposite. This species infects erythrocytes, monocytes and heterophils, inducing significant nuclear deformities. Phylogenetic analysis placed both Lankesterella sequences in a clade with other Lankesterella parasites from lizards, highlighting the genetic diversity of this genus within this host group. These findings expand the knowledge about parasitic biodiversity in Neotropical reptiles and underscore the necessity of integrating morphological and molecular methodologies to elucidate the taxonomy of understudied groups such as haemococcidians.