The cytochrome c oxidase subunit I (COI) gene has been used broadly as a DNA barcoding region or and relevant molecular marker for phylogenetic reconstruction. The exact region that has been standardized as a universal barcode is the one amplified by Folmer's primers HCO-LCO. Nevertheless, many other primers have been developed for the amplification of the COI gene, among them the Jerry-Pat primers. This paper aims to analyze the performance of different regions of the COI, in particular those amplified by Folmer's and Jerry-Pat primers, on different taxonomic levels by using specimens from a complex and homogeneous beetle family, Mordellidae Latreille, 1802. To achieve this goal, we used two different datasets: Jerry-Pat matrix included 48 sequences from specimens sampled in the field and 19 sequences from GenBank, whereas Folmer's matrix included 91 sequences from BOLD; representing 24 and 85 species respectively. Our results show different properties of both COI regions regarding GC content (3.7% lower in Jerry-Pat fragment), sequence length, interspecific divergence, evolutionary models, and saturation analyses. We also found that the two studied regions of the COI perform differently, showing notable differences in the topology of the reconstructed trees. Finally, a discussion of the pros and cons of each region is provided. This is a first glance at the molecular data of Mordellidae, where we provided a general picture of the evolutionary history of the family and included new sequences for Mediimorda Méquignon, 1946 and Stenalia Mulsant, 1856.