Domestic dogs may carry several vector-borne pathogens, including zoonotic agents, especially in tropical regions like Central America. The epidemiology of these pathogens is prone to change due to urbanization, trade and travel as well as climate change, necessitating repeated monitoring. This study aims to present a comprehensive picture of canine vector-borne diseases in Costa Rica, combining data on seroprevalence with molecular species identification of the causative pathogens. In this survey, 294 dogs from all seven provinces of Costa Rica were included. After a clinical examination, diagnostic blood samples were analyzed with regard to packed cell volume (PCV) and presence of microfilaria. Serum samples were tested for antibodies against
Ehrlichia
spp.,
Anaplasma
spp.,
Babesia
spp.,
Borrelia burgdorferi
sensu lato (s.l.) as well as antigen of
Dirofilaria immitis
. Seropositive and microfilaremic blood samples were analyzed by PCR to detect current infections and identify the pathogen species. Overall, 45.24% (133/294, 95% CI: 39.45–51.11%) of dogs were seropositive for at least one of the tested pathogens. Seroprevalence was highest for
Ehrlichia
spp. (39.46%, 116/294, 95% CI: 33.83–45.29%), followed by
Babesia
spp. (23.13%, 68/294, 95% CI: 18.43–28.38%),
Anaplasma
spp. (13.27%, 39/294, 95% CI: 9.61–17.69%), and
B. burgdorferi
s.l. (0.34%, 1/294, 95% CI: 0.01–1.88%). Generalized linear mixed models indicated a significant association of
Ehrlichia
-,
Anaplasma
- and
Babesia
-seropositivity, as well as a significant effect of age and breed on
Ehrlichia
-seropositivity. Furthermore, a statistically significant negative effect of
Ehrlichia
-,
Anaplasma
-, and
Babesia
-seropositivity on PCV was found. Regarding current infections,
Ehrlichia canis
DNA was detected in 51.72% (60/116, 95% CI: 42.26–61.10%) of
Ehrlichia
-seropositive dogs, while
Ehrlichia ewingii
and
Ehrlichia chaffeensis
were not detected. Furthermore, 10.26% (4/39, 95% CI: 2.87–24.22%) of
Anaplasma
-seropositive dogs were coinfected with
Anaplasma phagocytophilum
and
Anaplasma platys
, while one animal (2.56%, 95% CI: 0.65–13.48%) was infected with
A. phagocytophilum
only. Among
Babesia
-seropositive dogs,
Babesia vogeli
and
Hepatozoon canis
were detected in one animal each (1.47%, 1/68, 95% CI: 0.04–7.92%).
Dirofilaria immitis
antigen was detected in 4.42% (13/294, 95% CI: 2.38–7.44%) of dogs. In microfilare...