The present study was carried out from the month of March to December, 2016 and aimed to isolate and investigate the prevalence of Gallibacterium anatis infection as well as to study the antimicrobial susceptibility pattern of the bacterium from extensively reared local breed of female Muscovy ducks in Maiduguri, Northeastern Nigeria. To accomplish this, a total of 250 samples (100 tracheal swabs, 100 cloacal swabs and 50 part of ovary) were collected from households where Muscovy ducks are reared and female Muscovy ducks from live birds market. Microbiological isolation and biochemical identification of the phenotypic characteristic consistent with G. anatis was used for the diagnosis of a positive sample and this revealed 75/250 (30.0%) positive isolates of the bacterium. The G. anatis was more frequently isolated from samples collected from house hold Muscovy ducks 51 (20.40%) than those from the live birds market 24 (9.60%) with a significant difference (P < 0.0001 at 95% CI; RR= 1.302). However, isolates where more frequently cultivated in samples of the tracheal swab 49 (19.60%) than those swabs collected from the cloaca 24 (9.60%) and ovary 2 (0.80%). G. anatis was discovered to be more frequent in the rainy season 51 (20.40%) when compared to the dry season 24 (9.60%) with a significant difference (P = 0.0080 at 95% CI; RR = 0.8466). Moreover, isolates revealed positive reactions to test with catalase, oxidase, phosphatase, sucrose and sorbitol, but show negative reactions to indole, urease, coagulase and maltose. The biochemical investigations differentiated the isolated strains into two biovars; haemolytic Gallibacterium anatis biovar 3 (4.0%) and a non-haemolytic Gallibacterium anatis biovar 72 (96.0%). Antimicrobial susceptibility test revealed multi-drug resistant of the Gallibacterium anatis isolated. The in-vitro antibiotic susceptibility testing revealed that isolates were highly susceptible to Cefotaxime, moderately susceptible to Ciprofloxacin, Doxycycline and Florfenicol. In conclusion, G. anatis is prevalent in extensively reared local breed of Muscovy ducks in the study area. Therefore, strict biosecurity measures should be practiced at all level of poultry production systems to curb the spread of the organism. Antimicrobial abuse should be avoided by poultry farmers and the guidance of a registered veterinarian should be sought whenever there is need for medications to avoid misuse and drug resistance.