Introduction and purpose: The recent cholera spread, new cases, and fatality continue to arouse concern in public health systems; however, interventions on control is at its peak yet statistics show continuous report. This study characterized atypical and patho-significant environmentalVibrio choleraeretrieved from ground/surface/domestic water in rural-urban-sub-urban locations of Amathole District municipality and Chris Hani District municipality, Eastern Cape Province, South Africa.Methods: Domestic/surface water was sampled and 759 presumptiveV. choleraeisolates were retrieved using standard microbiological methods. Virulence phenotypic test: toxin co-regulated pili (tcp), choleragen red, protease production, lecithinase production, and lipase test were conducted. Serotyping using polyvalent antisera (Bengal and Ogawa/Inaba/Hikojima) and molecular typing: 16SrRNA, OmpW, serogroup (Vc-O1/O139), biotype (tcpAClas/El Tor,HlyAClas/El Tor,rstRClas/El Tor,RS1,rtxA,rtxC), and virulence (ctxA,ctxB,zot,ace,cep,prt,toxR,hlyA) genes were targeted.Result: Result of16SrRNAtyping confirmed 508 (66.9%) whileOmpWdetected/confirmed 61 (12.01%)V. choleraestrains. Phenotypic-biotyping scheme showed positive test to polymyxin B (68.9%), Voges proskauer (6.6%), and Bengal serology (11.5%). Whereas Vc-O1/O139 was negative, yet two of the isolates harbored the cholera toxin with a gene-typectxBandhlyAClas: 2/61, revealing atypical/unusual/dual biotype phenotypic/genotypic features. Other potential atypical genotypes detected includerstR: 7/61,Cep: 15/61,ace: 20/61,hlyAElTor: 53/61,rtxA: 30/61,rtxC: 11/61, andprtV: 15/61 respectively.Conclusion: Although additional patho-significant/virulent genotypes associated with epidemic/sporadic cholera cases were detected, an advanced, bioinformatics, and post-molecular evaluation is necessary. Such stride possesses potential to adequately minimize future cholera cases associated with dynamic/atypical environmentalV. choleraestrains.