Background: Panama is recognized as a global biodiversity hotspot; however, little is known about the genetic diversity patterns of Toxoplasma gondii in wildlife. This exploratory study evaluated the allelic and haplotypic diversity of the Alt. SAG2, GRA6, and Apico markers using wildlife tissue samples; additionally, it compared the genealogical relationships between the identified variants and a defined panel of reference sequences. Methods: Three cloned amplicons per tissue and locus were analyzed by bidirectional Sanger sequencing from 18 tissue samples collected from 13 wild animals. Locus-specific sequence relationships were examined using alignments, NeighborNet networks, and unrooted Neighbor-Joining trees based on p-distances. Results: A total of 162 clone sequences were generated, comprising 54 sequences for each locus. Alt.SAG2 variants clustered with reference alleles associated with T. gondii types II and III, whereas GRA6 variants clustered with reference alleles associated with type I, II, and III. The analyzed Apico fragment showed limited resolution among the three reference groups. Multiple sequence variants were recovered from some tissue-derived clone sets. Conclusions: The genetic variation detected in Panamanian wildlife comprises a heterogeneous set of T. gondii sequence variants associated with archetypal clonal variants and with sequence variants described in geographically distant regions. These findings suggest that the allelic variation present in the analyzed wildlife is not restricted to the regional context but is part of a broader pattern of T. gondii diversity in the Neotropics.