Scripture passages identifying the various men named "James" in the New Testament:

The Apostle James Zebedee (brother of the Apostle St. John) Matthew 4:21; 10:2-3; 17:1; 20:20-23; 26:37
Mark 1:19-20; 1:29; 3:17; 5:37; 9:2; 10:35, 41; 13:3; 14:33
Luke 5:10; ; 8:51; 9:28, 54
Acts 1:13; Acts 12:2
The Apostle James son of Alphaeus Matthew 10:3
Mark 3:18
Luke 6:15
Acts 1:13
James the "brother" of Jesus; Jesus' "brothers" in general Matthew 12:46-50; 13:55
Mark 3:21, 6:3
John 7:3-5
Acts 1:14
Galatians 1:19
James 1:1
James whose mother is Mary Matthew 27:56
Mark 15:40, 16:1
Luke 24:10
James, the "brother" of Jesus and Bishop of Jerusalem Acts 12:17; Acts 15:1315:13; 21:18
1 Corinthians 15:5-7
Galatians 1:19; 2:9, 12;
James 1:1
Jude 1:1
James, the father of the Apostle Jude Acts 1:13

Keep in mind, however, that more than one category may refer to the same man

Most scholars would agree that it is unlikely that James, the Bishop of Jerusalem, would have been the Apostle James Zebedee who was martyred circa AD 42 since James the Bishop is alive and active in the Church until his martyrdom circa AD 62 (or possibly sometime between 62 and 69) . That James the Just (or Righteous), Bishop of Jerusalem suffered martyrdom shortly before the destruction of the Temple and the holy city of Jerusalem by the Roman Army in AD 70 is confirmed by the Jewish 1st century  historian Flavius Josephus in his book, Antiquities of the Jews 20.9.1, when he places James' death after the death of the Roman governor Festus, but before the arrival of the new Roman governor Albinus: "Festus was now dead, and Albinus was but upon the road; so he [the High Priest Ananus] assembled the Sanhedrin of judges, and brought before them the brother of Jesus, who was called Christ, whose name was James, and some others, [or, some of his companions]; and when he had formed an accusation against them as breakers of the law, he delivered them to be stoned..."

There are scholars who believe that there were only two men named James who are mentioned in the New Testament and that the Apostle James son of Alphaeus, also known as James the Less to distinguish him from the Apostle James Zebedee [James the greater], is the son of the woman named Mary of Clopas as well as the brother/kinsmen of Jesus who was selected to be the first Christian Bishop of Jerusalem. It is true that the title "James the Less" is given to both James son of Alphaeus and James the Bishop but it is possible both men were identified as "the Less" to distinguish them from the elder and/or more important man in the hierarchy of the Apostles, James Zebedee. Those who identify James son of Alphaeus with James the son of Mary of Clopas assume that Alphaeus and Clopas were the same man, an assumption for which there is no Biblical evidence.

There are also those scholars who also assume that James son of Alphaeus is a brother of the Apostle Matthew/Levi since Mark 2:14 also identifies Matthew as the son of a man named Alphaeus. However, Alphaeus was a common name in the 1st century and nowhere in the Gospels or in the other books of the New Testament are Matthew and James son of Alphaeus ever identified as brothers. Since the Gospels identify Peter and Andrew as brothers/kinsmen and John and James as brothers and sons of Zebedee [Matthew 10:3], it seems strange that the Gospel writers would neglect to identify a kinship connection between two more Apostles. The manner in which James son of Alphaeus and Matthew/Levi are listed in the ranks of the twelve Apostles also does not suggest any connection between these two men but strongly indicates two different and non-related individuals. To identify these men as siblings reads into the text of the Gospels what is not there.

Another vague connection is often made by identifying Alphaeus with a man named Clopas [Acts 1:13], or identifying Clopas with Cleopas [Luke 24:18]. This connection is based on the confusion concerning the number of women disciples present at the Cross: three women in John 19:25 and four women in Matthew 27:56 and Mark 15:40. It is confusing for the reader because in the ancient text there are no clear grammatical helps like our modern commas, etc. so it is difficult to determine how many women are indicated in John 19:25: "Near the cross of Jesus stood his mother and his mother's sister Mary (the wife of) Clopas and Mary of Magdala. " There is simply no punctuation in the ancient koine Greek passage so we do not know if there are four women: the Virgin Mary, an unnamed kinswoman of the Virgin, Mary of Clopas (the literal text does not say "wife of"-Clopas could be her father or son or husband), and Mary of Magdala; or if there are there three women: The Virgin Mary, her "sister"/kinswoman Mary of Clopas, and Mary Magdala. Since the text provides no further information we must admit that the answer to that particular question cannot be answered. All we can say is that there are four women listed in Matthew 27:56 and in Mark 15:40 and in total probably at least eight women disciples present in Jerusalem when one includes references to Salome [Mark 15:40; 16:1], Joanna [Luke 8:3; 24:10], and Susannah [Luke 8:3], Mary and Martha the sisters of Lazarus [John 11:5; etc]. The problem with making Mary of Clopas the mother of James the son of Alphaeus and a cousin of Jesus is that this close relationship is not supported anywhere in the Scriptural text nor is it supported in the writing of the earliest Church fathers. Then too, there is no evidence that Alphaeus is a variation of Clopas in Aramaic, nor is there any evidence that the names Clopas [Klopas] and Cleopas [Kleopas] are related in Aramaic. Clopas is a Greek name of Semitic origin while Cleopas, which means "illustrious father," is the Greek masculine for the feminine Greek name Cleopatra. Cleopas was one of the two disciples Jesus joined after His Resurrection on the Road to Emmaus in Luke 24:8. Hegesippus, the Jewish Christian chronicler of early Church history, writes of a tradition that identifies Clopas as a kinsman/brother of Joseph of Nazareth. According to Hegesippus, Clopas was the father of Symeon [Simon] who was selected by the Apostles to succeed James as the Bishop of Jerusalem after James was martyred. [See Church History, Bishop Eusebius 3.11, 32; 4:22].

The identification of the Apostle James "the younger" or "the lesser" as a son of a man named Alphaeus who was also called Clopas and therefore a "brother" of Jesus is based upon three unsupported suppositions:

  1. The assumption that Mary of Clopas refers to the wife of Clopas. Since the text does not identify her as the "wife" of Clopas she could be Clopas' daughter or sister or even his mother.
  2. The assumption that Mary [wife, sister, daughter, or mother] of Clopas is the sister/kinswoman of the Virgin Mary.
  3. The assumption that James in Mark 15:40 is the same man as the James of Mark 3:18

These are too many unsupported assumptions to make to this theory credible.