In 2002, a new invasive pest ant in the genus, Nylanderia (formerly Paratrechina), was found in Houston, TX. This invasive ant has been causing significant economic and ecological damage in infested areas. Because of the morphological and behavioral similarities to Nylanderia pubens Forel (Caribbean crazy ant) found in Florida, this ant was named Nylanderia sp. nr. pubens (Rasberry crazy ant). So far, morphometric and phylogenetic analyses have not determined if the two ants are the same or separate species. To determine the relationships between the two populations, a molecular approach was undertaken. Five novel genes with various functions from N. pubens and N. sp. nr. pubens were cloned, sequenced, and identified, including a chemosensory protein (NpCsp), the cyclophilinlike protein (NpClp), the fatty acid binding protein (NpFabp), the ferritin 2-like protein (NpFlp), and an odorant binding protein (NpObp). The cDNA sequences of NpCsp, NpFabp, NpFlp, and NpObp, shared 100% identity between N. sp. nr. pubens and N. pubens. The cDNA of NpClp shared 99% identity, with the only difference at the nucleotide position 358. Comparisons of four partial genomic DNA sequences from Caribbean and Rasberry crazy ants indicated 100% identity for a 710-bp partial genomic DNA sequence of cytochrome oxidase subunit I gene, 99% identity for a 774 bp, and a 452-bp partial genomic DNA sequence of NpFabp and NpObp containing noncoding regions, and 100% identity for a 289 bp partial genomic DNA sequence of NpCsp containing only coding region. This study showed that N. sp. nr. pubens in Texas is the same, or at most an intraspecific variant or ecotype of the species in Florida.