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The avian pathogenic <i>Escherichia coli</i> (APEC) strains are the chief etiology of colibacillosis worldwide. The present study investigated the circulating phylotypes, existence of virulence genes (VGs), and antimicrobial resistance (AMR) in 392 APEC isolates, obtained from 130 samples belonged to six farms using both phenotypic and PCR-based molecular approaches. Congo red binding (CRB) assay confirmed 174 APEC isolates which were segregated into ten, nine, and eight distinct genotypes by RAPD assay (discriminatory index, DI = 0.8707), BOX-PCR (DI = 0.8591) and ERIC-PCR (DI = 0.8371), respectively. The combination of three phylogenetic markers (<i>chu</i>A, <i>yja</i>A and DNA fragment TspE4.C2) classified APEC isolates into B2₃ (37.36%), A1 (33.91%), D2 (11.49%), B2₂ (9.20%), and B1 (8.05%) phylotypes. Majority of the APEC isolates (75–100%) harbored VGs (<i>ial</i>, <i>fim</i>H, <i>crl</i>, <i>pap</i>C, and <i>cjr</i>C). These VGs (<i>pap</i>C and <i>cjr</i>C) and phylotypes (D2 and B2) of APEC had significant (<i>p</i> = 0.004) association with colibacillosis. Phylogenetic analysis showed two distinct clades (clade A and clade B) of APEC, where clade A had 98–100% similarity with <i>E. coli</i> APEC O78 and <i>E. coli</i> EHEC strains, and clade B had closest relationship with <i>E. coli</i> O169:H41 strain. Interestingly, phylogroups B2 and D2 were found in the APEC strains of both clades, while the strains from phylogroups A1 and B1 were found in clade A only. In this study, 81.71% of the isolates were biofilm formers, and possessed plasmids of varying ranges (1.0 to 54 kb). <i>In vitro</i> antibiogram profiling revealed that 100% isolates were resistant to ≥3 antibiotics, of which 61.96%, 55.24%, 53.85%, 51.16% and 45.58% isolates in phylotypes B1, D2, B2₂, B2₃, and A1, respectively, were resistant to these antimicrobials. The resistance patterns varied among different phylotypes, notably in phylotype B2₂, showing the highest resistance to ampicillin (90.91%), nalidixic acid (90.11%), tetracycline (83.72%), and nitrofurantoin (65.12%). Correspondence analysis also showed significant correlation among phylotypes with CRB (<i>p</i> = 0.008), biofilm formation (<i>p</i> = 0.02), drug resistance (<i>p</i> = 0.03), and VGs (<i>p</i> = 0.06). This report demonstrated that B2 and A1 phylotypes are dominantly circulating APEC phylotypes in Bangladesh; however, B2 and D2 are strongly associated with the pathogenicity. A high prevalence of antibiotic-resistant APEC strains from different phylotypes suggest the use of organic antimicrobial compounds, and/or metals, and the rotational use of antibiotics in poultry farms in Bangladesh.