In recent years, the recording of fish with vertebral malformations has attracted growing interest worldwide, as these malformations may be associated with exposure to xenobiotics. This study aimed to determine the presence and concentrations of pesticide residues (organochlorines and organophosphates) in coastal fish in Nayarit, Mexico, and to assess their potential association with vertebral malformations. From November 2013 to September 2021, 32 fish, with visible malformations were conveniently collected, an equal number of healthy specimens per species was selected for comparative analysis. The fish exhibited vertebral malformations of the following types: kyphosis, lordosis, and scoliosis in 9, 8 and 6 species, respectively, while the total number of malformations was higher across the sampled organisms. Furthermore, pesticide residues were detected in both healthy and malformed fish using gas chromatography coupled with tandem mass spectrometry (GC-MS/MS). The samples analyzed contained at least one pesticide, with the group of healthy fish showing greater diversity of organochlorine compounds. The most frequent of these were p,p’-DDE, followed by p,p’-DDT (41%), p,p’-DDD (25%), and endrin (25%). The species C. raredonae and A. seemanni exhibited the greatest number of pesticides. The pesticides observed in malformed fish samples were p,p’-DDE (100%), p,p’-DDD (97%), p,p’-DDT (97%), endrin (50%), and BHC delta (31%). Chlorpyrifos was present (56% and 100% in healthy and malformed fish), with the highest frequency observed in A. seemanni and B. panamensis. The highest concentrations were observed in the DDT group. An association was also observed between vertebral malformations and concentrations of p,p’-DDE and chlorpyrifos in the species C. raredonae and A. guatemalensis. Multivariate analysis revealed a clear separation between malformed and healthy fish based on contaminant profiles.