Background The emergence and spread of antimicrobial resistance (AMR) among uropathogens is increasing, especially in resource limited settings due to a number of reasons. The emergence of drug resistance and particularly the production of Extended Spectrum β-Lactamase (ESBL) by some strains of E. coli and methicillin resistance of Staphylococcus species, limits the choice of antimicrobials in the treatment of urinary tract infection (UTI). However, little is known about the bacteriology of UTI among pregnant women in Hargeisa, SomalilandMethods A cross-sectional study was conducted in the period of 1 Feb to 30 May 2019 among pregnant women at Edna Adan Hospital (EAH), Hargeisa. Following the standard procedure, clean-catch mid-stream urine samples were collected and processed for bacteriological culture. A urine sample was considered positive for significant bacteriuria (SBU) when a single organism was cultured at a concentration of ≥ 105 Colony Forming Units/ml. Antimicrobial sensitivity testing (AST) was done using Kirby-Bauer disc diffusion technique. Ceftazidime (30 µg) and Cefotaxime (30 µg) disks were used for ESBL screening as per CLSI guideline and each ESBL screening positive isolate were phenotypically confirmed by a combination disk test.Results Among 376 study participants, 79 (21.0%) had SBU. Majority at 58(73.4%) of the isolates were Gram-negative. The most predominant isolate was E.coli at 36(45.6%) followed by K. pneumonea 16(20.3%) and S. aureus at 9(11.4%). The proportion of ESBL producing isolates was at 25(32.9%). Gram-negative bacteria showed high level resistance to ampicillin, amoxicillin, cefotaxime, and cephalexin at 87%, 85%, 57%, and 52%, respectively. Previous history of UTI, monthly income, educational status and having dysuria were significantly associated with SBU (p < 0.05).Conclusions Most of the isolates were found resistant to the commonly prescribed antimicrobial drugs. Therefore, actions to minimize AMR should be in place to reduce the impact of urinary tract infections among pregnant women. Future large scale study is warranted to find out bacteriological and other factors associated with ESBL producing uropathogenes.