Cholera continued to be a major diarrheal illness in Nepal and antibiotic resistance has appeared as a serious problem in cholera management. The study aimed at analyzing the distribution pattern of the resistotypes (R-types) of Vibrio cholerae in the Kathmandu valley, Nepal. During June 2008 to January 2009, 210 diarrheal specimens received at National Public Health Laboratory from suspected cholera patients were subjected to standard bacteriological investigation including biotyping and serotyping. Antimicrobial susceptibility pattern of V. cholerae isolates was determined by Kirby Bauer disc diffusion method following CLSI guidelines. A total of 57 (27%) V. cholerae isolated were recovered, all of which belonged to 01 Ogawa Biotype EL Tor. Based on antibiogram, V. cholerae isolates in our study revealed three distinct R-types: R-type I, R-type II and R-type III. All three R types showed resistance to furazolidone, nalidixic acid and cotrimoxazole while sensitive to ciprofloxacin and tetracycline. Additional resistance to ampicillin and erythromycin was observed respectively in R-type II and III. Different R-types showed unique month wise variations (P < 0.05). Differentiation of V. cholerae strains into R-types is an important tool. In addition to direct patient management, it may have implication in identifying the source and spread of infection, and understanding the distribution pattern in a particular geographical region.