Several vector-borne pathogens restrict livestock farming and have significant economic impact worldwide. In endemic areas livestock are exposed to different tick species carrying various pathogens which could result in co-infection with several tick-borne pathogens in a single host. Although the co-infection of and the interaction among pathogens are critical factors to determine the disease outcome, pathogen interactions in the vector and the host are poorly understood. In this study, we surveyed the presence of
Babesia ovis
,
Theileria ovis
,
Theileria lestoquardi
,
Anaplasma ovis
,
Anaplasma phagocytophilum
, and
Anaplasma marginale
in 200 goats from 3 different districts in Sistan and Baluchestan province, Iran. Species-specific diagnostic PCRs and sequence analysis revealed that 1.5%, 12.5%, and 80% of samples were positive for
T
.
lestoquardi
,
T
.
ovis
, and
A
.
ovis
, respectively. Co-infections of goats with up to 3 pathogens were seen in 22% of the samples. We detected a significant association between
T
.
ovis
infection and age,
T
.
ovis
infection and location (Zabol), and
A
.
ovis
infection and location (Sarbaz) by multivariate logistic regression analysis. In addition, by analyzing the data with respect to
Plasmodium caprae
infection in these goats, a negative correlation was found between
P
.
caprae
and
A
.
ovis
infection. This study contributes to understanding the epidemiology of vector-borne pathogens and their interplay in goats.