Meningococcal disease in Mexico has a very low incidence; it is one of the countries with few reported cases as prevalence of the carrier state is unknown. Some studies have shown that many invasive meningococcal diseases are restricted to a specific number of hyper-virulent strains that contrast with carrier isolates. The aim of this study was to determine the frequency and characterization of meningococcal carriage isolates among prisoner's inmates. Nasopharyngeal swabs were obtained, Neisseria meningitidis was identified by standard methods, Polymerase Chain Reaction, and penicillin susceptibility was carried out. Multilocus Sequence Typing was performed as well. The study included 461 inmates. The overall carrier frequency was 10.41%, serogroups were isolated: B (20), C (17), Y (8) and nongroupable (3), 70.8% (34/48) of isolates showed some level of resistance to penicillin. Genetic diversity among isolates is observed and the presence of hypervirulent clones was demonstrated as ST42/44 CC and ST11/ET37CC.