Cyanobacterial harmful algal blooms (CyanoHABs) are observed in many regions worldwide with increasing frequency. The massive development of cyanobacteria is a severe problem for the water environment due to negative changes in water parameters, the introduction of toxic metabolites (cyanotoxins) into the water, and the resulting disruption of ecological relations in the ecosystem. Knowledge regarding CyanoHABs in aquatic reservoirs is increasing. However, information about cyanobacteria development in other, untypical habitats like deserts, open soils, or polar regions is still insufficient. Similarly, data regarding the distribution of cyanotoxins are extensive for some regions (for example, in Europe or North America), whereas, in other localities, such as those in South America, the data are scarce. In this paper, we investigated if phototrophic microbial communities collected from open soil (La Paz department, Sud Yungas province, Bolivia) contained cyanobacteria described as cyanotoxin producers. We performed qualitative and quantitative analysis of typical cyanotoxins found in aquatic reservoirs – anatoxin-a (ATX-a), cylindrospermopsin (CYN), and microcystin-LR (MC-LR). The obtained results showed a relatively high biodiversity of the studied microbial phototrophic community, which consists of several cyanobacterial and algal genera. Analyses of cyanotoxins showed that CYN and MC-LR were not present in the studied samples. However, despite the lack of cyanobacteria described as ATX-a producers, high-performance liquid chromatography (HPLC) chromatograms were revealed, and mass spectrometry (MS) spectra confirmed the presence of the toxin in the studied material. The results presented in this paper are, to the best of our knowledge, the first confirmation of the presence of ATX-a in open soil habitats, as well as the first record of cyanotoxin occurrence in Bolivia. The identification of anatoxin-producing cyanobacteria in open soil environments presents a novel finding that necessitates further work to elucidate their prevalence, abundance, and associated potential hazards, as well as the taxonomic classification of the specific cyanobacterial species able for anatoxin synthesis within these soil habitats. Future studies should focus on the distribution of cyanotoxins in cyanobacterial communities in untypical habitats and in localities for which, to date, the information on cyanotoxin occurrence is not currently available.