The poultry industry faces a significant challenge from avian pathogenic Escherichia coli (APEC), posing a threat to food safety chains and resulting in substantial financial losses. We aim to investigate the association of genotypic and phenotypic resistance with the phylogenetic group and virulence genotype in APEC isolated from clinical cases of colibacillosis in commercial broiler, layer, and breeder chickens. We used logistic regression to identify associations among resistance and susceptibility to antibiotic agents, virulence and phylogenetic groups of APEC isolates. The study revealed a significant association between resistance or susceptibility to antibiotic agents (neomycin, ceftriaxone, chloramphenicol, cotrimoxazole and doxycycline) with the phylogenetic groups of APEC isolates, particularly with a high association with phylogenetic group B1. The phylogenetic groups C, D, and E clade were associated with levofloxacin, cotrimoxazole, and doxycycline susceptibility. The most prevalent virulence associated genes (VAGs) (fimH, issa , traTa , sit.chr., kpsII, issb , and cvi.cva) in APEC were equally associated with all phylogenetic groups. The carriage of these prevalent genes were significantly associated with phylogenetic group D and E (16 gene out of 57 tested). Additionally, the carriage of sfa.foc was significantly associated with B2. qnrA genes and tetB genes were significantly associated with isolates positive for VAGs. Commercial broiler, layer, and breeder chickens in Nepal harbored APEC with varying susceptibility to the tested antimicrobials, with the majority being resistant to commonly used antibiotics. Most APEC isolates from these chickens may act as reservoirs for antibiotic resistance genes (ARGs), with the colistin resistant gene mcr1 being the most predominantly detected gene. The work highlights the importance of exploring the interconnections between virulence genotype, genetic background, and antimicrobial resistance (AMR) in APEC strains. It is noteworthy that ARGs and phenotypic resistance alone may not determine AMR due to their inverse relationship, indicating that these chickens could be potential reservoirs for antibiotic resistant APEC. Such insights are crucial for addressing challenges related intriguing VAGs, AMR of poultry production, as well as ensuring food safety and public health.