Columnaris is a common flavobacterial disease affecting tilapia aquaculture. Flavobacterium columnare has been identified as being responsible for the heavy mortalities of earthen-pond-cultured Nile tilapia (Oreochromis niloticus) at the Fayoum Governorate, Egypt. Mortalities have been closely associated with bad husbandry in the overstocked ponds. Diseased fish showed fin and tail rot with a thick yellowish turbid mucus covering the affected skin and gills. Scanning electron microscopy revealed the presence of numerous bacterial cells dispersed in the affected gill tissues. Most of the investigated specimens (60%) were infected with F. columnare. Forty-seven bacterial isolates were phenotypically identified based on cultural and biochemical characteristics. Molecular identification, virulence property assessment, and antibiotic-sensitivity testing were performed on 10 randomly selected isolates. The identities of the isolates were confirmed by gene sequence and phylogenetic analyses. These isolates yielded variable results regarding virulence genes (gtf, norB, and trx) and ability to adhere to fish gills. All isolates exhibited proteolytic and chondroitin lyase activities but had different antibiotic-sensitivity profiles. The pathogenicity of one highly pathogenic isolate was tested via intramuscular injection into juvenile O. niloticus. The challenged fish showed fin rot and skin ulceration with 80% cumulative mortalities. The study discussed critical points in the pathogenesis of columnaris disease affecting Nile tilapia that may help to find out effective control measures and refers to the need for prudent use of antimicrobials in aquaculture to protect aquatic animals and human health.