Culicidae mosquitoes are potential vectors of pathogens that affect human health. The correct species identification, as well as the discovery and description of cryptic species, is important in public health for the control and management of specific vectors. In the present study, the diversity of anthropophagous mosquitoes in Quintana Roo, at the border between Mexico and Belize, was evaluated using morphological and molecular data (COI‐DNA Barcoding). A total of 1,413 adult female specimens were collected, belonging to eight genera and 31 morphospecies. Most species formed well‐supported clades. Intraspecific Kimura 2 parameters (K2P) distance average was 0.75%, and a maximum distance of 4.40% was observed for
Anopheles crucians
s.l. ABGD method identified 28 entities, while 32 entities were identified with the BIN system. In
Culex interrogator
and
Culex nigripalpus
a low interspecific genetic distance of 0.1% was observed. One undescribed species belonging to the genus
Aedes
(
Aedes
n. sp.) was discovered, but no clear genetic divergence was found between this species and the closely related species
Aedes angustivittatus
. An intraspecific K2P distance greater than 2.7% was observed in
Aedes serratus
(3.9%),
Anopheles crucians
s.l. (4.4%),
Culex taeniopus
(3.7%),
Haemagogus equinus
(3.9%),
Culex erraticus
(5.0%),
Psorophora ferox
(4.5%), and in
Anopheles apicimacula
(8.10%); therefore, evidences of cryptic diversity are shown in these species. This study showed that DNA barcodes offer a reliable framework for mosquito species identification in Quintana Roo, except for some closely related species for which it is recommended to use additional nuclear genetic markers such as ITS2, in order to resolve these small discrepancies.