Blastocystisis a common intestinal protist with a global distribution in humans and many other animals. Yet, the status ofBlastocystisas a pathogen, the risk factors associated with its transmission, and its zoonotic potential remain ill-defined. Here, we explored subtype (ST) diversity and potential risk factors forBlastocystisinfection in 98 children from Apulo, Colombia. Samples were screened forBlastocystisvia PCR, and ST identification was performed through next-generation amplicon sequencing (NGS). Associations between the presence ofBlastocystisand individual STs and sociodemographic variables were assessed via logistic regression analyses. Seventy-one samples (72.4%) wereBlastocystis-positive, and NGS revealed the presence of five STs (ST1-ST5). ST1, ST2, and ST3 were common and observed in nearly equal proportions (~ 40%), while samples with ST4 (1.4%) and ST5 (5.6%) were comparatively rare. The presence of mixed STs in the same sample was also common (28.2%). Comparisons among children within the same household identified that shared ST profiles were common, but diversity within family units was also observed. Logistic regression analyses returned significant associations between the presence ofBlastocystis, individual subtypes, or mixed subtypes for several variables. Intriguingly, the presence of animals was one of the most common significant associations. Taken together, these data represent an important step forward in understanding both the potential routes and risk factors that may influenceBlastocystistransmission and will be useful in shaping future studies which seek to clarify the relationships between STs, pathogenicity, and zoonotic transmission.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00436-023-07841-3.