This study utilized next-generation sequencing (NGS) of nrDNA ITS regions (ITS1 and ITS2) for the first time to analyze three honey samples from Anzer (Ballıköy), Rize province, Türkiye. The NGS results were evaluated alongside melissopalynological data. Pollen grains were first isolated and identified microscopically, and DNA was extracted from the honey samples for NGS analysis. ITS1 and ITS2 regions were sequenced using Illumina MiSeq, and results were compared with a custom reference library. NGS produced 310,745 paired-end reads for ITS1 and 39,835 reads for ITS2. Of these, 75.2% of ITS1 reads and 68.4% of ITS2 reads were identified to at least the family level. NGS analysis detected 27 plant families and 54 taxa, a 37% increase in taxa detection compared to melissopalynology, which identified 19 families and 34 taxa. Both approaches consistently identified dominant floral components, with NGS providing greater species-level resolution. Spearman’s correlation revealed a moderate linear relation between the two methodologies for two of the three samples. However, the Shannon-Wiener and Pielou indices were lower in metabarcoding than in melissopalynology due to the uneven distribution of read counts for some species. The R-coefficient results of all the families for the three samples showed over or underrepresentation except for Caryophyllaceae (honey sample ZT2 = 0.85) and Asteraceae (honey sample ZT3 = 0.93). While to date, melissopalynolgy has been the prime identification method for determining the geographical origin of honey, this study, for the first time, presents a comprehensive and reliable metabarcoding data for Anzer honey identification.