Ticks transmit the greater variety of pathogens of public and veterinary health importance. The diversity of tick-borne pathogens in the Caribbean is little known. We report here on the detection of tick-borne pathogens in individual Caribbean ticks by using a combination of NGS and high-throughput microfluidic real-time PCRs. Of 27,544 NGS contigs generated from 588 ticks collected in Guadeloupe and Martinique (Amblyomma variegatum, Rhipicephalus microplus), 1, 2 and 30% matched viral, bacterial and parasitic sequences, respectively. No known pathogenic viruses were detected. However, four new viruses were discovered, of which, one is a suspected human pathogen. Five bacterial genus were identified: Rickettsia, Coxiella, Anaplasma, Borrelia and Ehrlichia. At the species level, only Rickettsia africae (human) and Anaplasma marginale (bovine) were consistently detected. Two parasite genus were found, Babesia and Theileria, but only Babesia bigemina, a bovine pathogen was further identified. The prevalence of tick-borne pathogens was determined using the BioMarkTM dynamic arrays allowing the simultaneous detection of 30 bacterial, 17 parasitic and 22 viral species in 94 individual ticks. Of the four interesting viruses found by NGS, one was preferentially found in Amblyomma (23%) while the others were preferentially in Rhipicephalus (30-90%, no differences between Guadeloupe and Martinique). Rickettsia africae (96% Amblyomma), Ehrlichia ruminantium (5.1% Amblyomma) and Anaplasma marginale (4 to 40% Rhipicephalus) were the most detected bacteria. Babesia bigemina (1 to 12% Rhipicephalus) and Babesia bovis (0.7% Rhipicephalus), Theleria velifera (25% Rhipicephalus and 42% Amblyomma) and Theleria mutans (1.5-2% in both ticks), all pathogens of bovine, were also identified. Co-infections were frequent, with more than 10% and 2% of the ticks hosting 2 and 3 pathogens, respectively. Eleven and one ticks were infected with 4 and 5 different pathogens, respectively. These res