Population genetics is a scientific discipline which contributes to the examination of the human evolutionary and historical migrations. Particularly useful information is provided by the research of two uniparental markers within our genome, the Y-chromosome (Y-DNA) and mitochondrial DNA (mtDNA), as well as autosomal DNA. The data from Y-DNA and autosomal DNA suggests that the Croats mostly are descendants of the early Slavs of the medieval migration period, according to mtDNA have genetic diversity which fits within a broader European maternal genetic landscape, and overall have a uniformity with other South Slavs from the territory of former Yugoslavia.

There are many Paleolithic period sites located in the territory of Croatia, mostly ascribed to the Mousterian phase in the Middle Paleolithic period. In the Neolithic period in Southeast Europe were founded major cultures like Vinča, Varna, Starčevo. In the Bronze Age happened symbiosis between Proto-Indo-Europeans of Kurgan culture and autochthonous populations, leading to the formation among others also of Proto-Illyrians. They gradually mixed and were assimilated by the Romans, Celts, Ostrogoths, and finally Early Slavs since the late 6th century.

In the 2014 study, of the three successfully generated SNP profiles of Neolithic Starčevo culture samples from Vinkovci, two belonged to Y-DNA haplogroup G2a-P15 and one to I2a1-P37.2, which could indicate G2a as a potential representative of the spread of farming from the Near East to Europe, while I2a as a Mesolithic substratum in Europe. In the 2018 study, 10 out of 17 samples from Croatia had a successful Y-DNA sequencing; two Croatia Cardial Neolithic (6005–5786 BCE) samples from Zemunica Cave belonged to C1a2 and E1b1b1a1b1, Early-Neolithic Starčevo culture (5837–5659 BCE) from Beli Manastir-Popova zemlja to C, Early-Neolithic Croatia Impressa culture (5641–5560 BCE) from Kargadur to G2a2a1, two Middle-Neolithic Sopot culture (5207–4546 BCE) samples from Osijek to G2a2a1 and J2a1, Late-Neolithic Sopot (4790–4558 BCE) from Beli Manastir-Popova zemlja to I, two Vučedol culture (2884–2582 BCE) samples from Beli Manastir-Popova zemlja and Vučedol Tell to R1b1a1a2a2 and G2a2a1a2a, and the Early-Middle Bronze Age (1631–1521 BCE) sample from Veliki Vanik belonged to J2b2a.

In the 2021, was made a genome-wide analysis on 38 out of 41 individuals from the 6200 years old massacre at village Potočani in Eastern Croatia. They belonged to the Middle Copper Age Lasinja culture, and autosomally 70% of them were not in close kinship implying "a community composed of many family groups". According to Admixture and PCA it revealed "that the analyzed individuals are slightly shifted from the Anatolia Neolithic cluster in the direction of Western European hunter-gatherers, similar to other Middle to Late Neolithic European farmers before the arrival of [Western] steppe ancestry", as on average had approximately 91% Anatolian Neolithic Farmers (ANF) and 9% Western Hunter-Gatherer (WHG)-related ancestry, being very distant from modern Croats. Among them were present "paternal lineages typical of Balkan Neolithic populations (eleven G2a2, two I2a1a(xI2a1a2), one I2a2, C and C1a2-V20)".

In the same year were analyzed additional 19 Middle Neolithic of Sopot culture, 1 Copper Age and 1 Roman age sample from Beli Manastir-Popova zemlja as well as 7 Bronze Age samples of Transdanubian Encrusted Pottery culture from Jagodnjak-Krčevine in Eastern Croatia. According to Admixture, Croatian Neolithic samples have 97.6-100% ANF-ancestry, Copper Age samples have 71% ANF-ancestry and 29% Western Steppe Herders (WSH)-ancestry, while Bronze Age samples 47% ANF, 20% WHG and 33% WSG-ancestry. The observed Y-DNA haplogroups in the Neolithic/Copper period were two G2a2a-PF3147, one G2a2b2a1a1-PF3345, one C1a2b-Z38888, two I2a2a-M223 and one J-M304; in the Bronze period were only four G2a2a1a2a2a1-Z31430 and one G2a2a1-PF3148. The one Roman period individual from 260 to 402 CE, "who may or may not be representative for the wider population in that time period", had an autosomal genetic combination very similar to present-day Southeastern Europeans (including Croats), "adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today". He carried Scythian-Eurasian Y-DNA haplogroup R1a1a1b2a2-Z2124 > R1a1a1b2a2b1-F1345 (R-F1019* subclade). Between 2018 and 2022 studies analyzed many samples related to the Cetina culture, Proto-Illyrians and specific Illyrian tribes (Iapydes and Liburni), finding that their paternal lineage almost exclusively belonged to the J2b-L283 haplogroup. Two years later, a study was published on 33 ancient samples from the 3rd to 5th centuries from the island of Hvar, and they had Y-DNA haplogroups, in order of frequency, J2a, E1b, J2b, and G2a.

In 2025 seven 3rd-century males from Roman period Mursa (today's Osijek) were analyzed, Roman soldiers but "none of them show genetic continuity with the preceding local Early Iron Age population", with their Y-DNA haplogroups being N1a-L550, R1b-S497, I2a-M223 > L701, and I1a-Z63 > S2077. In 2019 were autosomally analyzed three 5th-century individuals with artificial cranial deformation from Osijek, probably of Hunnic or Germanic origin. According to Principal component analysis and Admixture methods, one of them had East/Northeast Asian, another European/Caucasian, and the third Near Middle Eastern/North African ancestry.

A 2022 archaeogenetic study published in Science compared ancient, medieval, and modern Balkans population samples and found that the medieval Slavic migrations "profoundly affected the region", resulting in the reduction of Anatolian Neolithic ancestry in Southeastern Europe. Pre-Slavic Balkan populations have the most of the Anatolian Neolithic component of ancestry, whereas present-day Slavs outside the Balkans have the least, "with present-day people from Southeastern Europe", including Croats, "intermediate between the two extremes", with Greeks and Albanians having the most while Croats and Hungarians the least. A 2023 archaeogenetic study published in Cell confirmed that the spread of Slavic language and identity was because of large movements of people of both males and females with specific Eastern European ancestry and that "more than half of the ancestry of most peoples in the Balkans today comes from the Slavic migrations, with around a third Slavic ancestry even in countries like Greece where no Slavic languages are spoken today". The pre-Slavic period population of Croatia and the region had Y-DNA haplogroups E-V13, R1b, J2b, J2a, G2a while with Slavic migration arrived R1a-Z282 and I2a-L621 among others. The most comprehensive archaeogenetic study until now about the origin and spread of the early Slavs, published 2025 in Nature including 115 samples from pre-Slavic and Slavic period in Croatia, confirmed previous conclusions.

Genetically, on the paternal Y chromosome line and studies published between 2003 and 2008, a majority (>75%) of male Croats from Croatia belongs to one of the three major European Y-DNA haplogroups – I2 (32%-34%), R1a (27%-34%) and R1b (12%-15%), while a minority (>25%) belongs to haplogroups E (9%), I1 (5%-9%), J (4%), N (2%), and G (1%). According to recent and more extensive studies published between 2012 and 2022, a majority (65%) of male Croats from Croatia belongs to haplogroups I2 (39%-40%) and R1a (22%-24%), while a minority (35%) belongs to haplogroups E (10%), R1b (6%-7%), J (6%-7%), I1 (5-8%), G (2%), Q (0-1.93%), H (0-1.8%), T (0.6%), N (0-0.6%) and L (0.2%).