Anaplasmataceae agents are obligatory intracellular Gram-negative α-proteobacteria that are transmitted mostly by arthropod vectors. Although mammals of the Superorder Xenarthra (sloths, anteaters, and armadillos) have been implicated as reservoirs for several zoonotic agents, only few studies have sought to detect Anaplasmataceae agents in this group of mammals. This study aimed to investigate the occurrence and genetic diversity of
Anaplasma
spp. and
Ehrlichia
spp. in blood and spleen samples of free-living Xenarthra from four different states in Brazil (São Paulo, Mato Grosso do Sul, Rondônia, and Pará). Nested and conventional PCR screening assays were performed to detect the
rrs
and
dsb
genes of
Anaplasma
spp. and
Ehrlichia
spp., respectively. The assays were positive in 27.57% (91/330) of the
Anaplasma
spp. and 24.54% (81/330) of the
Ehrlichia
spp. Of the 91 positive
Anaplasma
spp. samples, 56.04% were positive in a conventional PCR assay targeting the 23S–5S intergenic region. Phylogenetic and distance analyses based on the
rrs
gene allocated
Anaplasma
sequences from sloths captured in Rondônia and Pará states in a single clade, which was closely related to the
A. marginale
,
A. ovis,
and
A. capra
clades. The sequences detected in southern anteaters from São Paulo were allocated in a clade closely related to sequences of
Anaplasma
spp. detected in
Nasua nasua
,
Leopardus pardalis
, and
Cerdocyon thous
in Brazil. These sequences were positioned close to
A. odocoilei
sequences. Genotype analysis corroborated previous findings and demonstrated the circulation of two distinct
Anaplasma
genotypes in animals from north and southeast Brazil. The first genotype was new. The second was previously detected in
N. nasua
in Mato Grosso do Sul state. The intergenic region analyses also demonstrated two distinct genotypes of
Anaplasma
. The sequences detected in Xenarthra from Pará and Rondônia states were closely related to those in
A. marginale
,
A. ovis,
and
A. capra
.
Anaplasma
spp. sequences detected in Xenarthra from São Paulo and were allocated close to those in
A. phagocytophilum
. The analyses based on the
dsb
gene grouped the
Ehrlichia
spp. sequences with sequences of
E. canis
(São Paulo, Mato Grosso do Sul, and Pará) and
E. minasensis
(Rondônia and Pará). The data indicate the occurrence of
E....