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Internally-displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a novel field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly-stigmatized group, internally-displaced people who inject drugs (IDPWID). We inform the framework by Nanopore generated HIVpolsequences and IDPWID migration history. In June-September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly-available sequences (N=359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data show that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.SIGNIFICANCE STATEMENTAs human displacement is on the rise globally, it is crucial to develop ways in which infectious disease transmission can be monitored in displaced populations. We tested a new molecular epidemiology framework that relies on molecular epidemiology methods and portable HIV sequencing from samples collected from a hard-to-reach population of internally-displaced people who inject drugs (IDPWID). We show that by phylogenetically identifying potential HIV transmission clusters, estimating times of the clusters’ origin, and referencing these times against the time of IDPWID’s arrival to a new region, we can estimate an approximate window during an IDPWID’s displacement journey when HIV transmissions are likely to happen. Further analysis indicated that HIV is primarily transmitted from local populations to IDPWID.